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1 Nova Hedwigia 86 1—2 1—21 Stuttgart, February 2008 DOI: 10.1127/0029-5035/2008/0086-0001 0029-5035/08/0086-0001 $ 5.25 © 2008 J. Cramer in der Gebrüder Borntraeger Verlagsbuchhandlung, D-14129 Berlin · D-70176 Stuttgart A morpho-molecular classification of the mosses (Bryophyta) by Michael Stech 1 and Wolfgang Frey 2 1 Nationaal Herbarium Nederland, Universiteit Leiden branch, P.O. Box 9514, 2300 RA Leiden, The Netherlands. E-mail [email protected] 2 Institut für Biologie - Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, Altensteinstr. 6, D-14195 Berlin, Germany With 1 figure and 2 tables Stech, M. & W. Frey (2008): A morpho-molecular classification of the mosses (Bryophyta). Nova Hedwigia 86: 1-21. Abstract: Molecular relationships within the Bryopsida are inferred from a new approach, i.e., the combined analysis of solely non-coding plastid markers (trnL UAA intron, atpB-rbcL spacer, psbA- trnH spacer). The current state of moss systematics is discussed with respect to the impact of this approach as well as other recently published molecular phylogenies and phylogenomic inferences. Taking into account the progress that has been made in the last few years by analysing molecular and non-molecular data, a new synopsis of the suprageneric classification of the Bryophyta is presented. Taxonomic changes comprise a re-evaluation of the taxonomy of Takakia (including Takakiophytina stat. nov.), Gigaspermidae subclass. nov., elevation of subfamilies of Dicranaceae to family level (Amphidiaceae stat. nov., Dicranellaceae stat. nov., Oncophoraceae stat. nov.), Hypodontiaceae fam. nov. and Helicophyllales ord. nov. Key words: Bryophyta, suprageneric classification, molecular phylogeny, trnL UAA intron, atpB-rbcL spacer, psbA-trnH spacer. Introduction Mosses form the second largest of the major land plant lineages. They comprise approximately 12,800 species (Crosby et al. 1999) and exhibit a high morphological and ecological diversity. Traditionally, the three groups of bryophytes (mosses, liverworts and hornworts) were treated as classes of the division Bryophyta. Molecular data, however, revealed that bryophytes are paraphyletic, with liverworts being sister to all other extant land plants, and mosses sister to a clade of hornworts and vascular plants (Qiu et al. 2006). As the three bryophyte groups obviously represent independent lineages in land plant evolution, it is now widely accepted to treat them as separate divisions, Bryophyta (mosses), Marchantiophyta (liverworts) and Anthocerotophyta

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1

Nova Hedwigia 86 1mdash2 1mdash21 Stuttgart February 2008

DOI 1011270029-503520080086-0001 0029-5035080086-0001 $ 525copy 2008 J Cramer in der Gebruumlder Borntraeger

Verlagsbuchhandlung D-14129 Berlin middot D-70176 Stuttgart

A morpho-molecular classification of the mosses (Bryophyta)

by

Michael Stech1 and Wolfgang Frey2

1Nationaal Herbarium Nederland Universiteit Leiden branch PO Box 9514 2300 RA LeidenThe Netherlands E-mail stechnhnleidenunivnl

2Institut fuumlr Biologie - Systematische Botanik und Pflanzengeographie Freie Universitaumlt BerlinAltensteinstr 6 D-14195 Berlin Germany

With 1 figure and 2 tables

Stech M amp W Frey (2008) A morpho-molecular classification of the mosses (Bryophyta) NovaHedwigia 86 1-21

Abstract Molecular relationships within the Bryopsida are inferred from a new approach ie thecombined analysis of solely non-coding plastid markers (trnL

UAA intron atpB-rbcL spacer psbA-

trnH spacer) The current state of moss systematics is discussed with respect to the impact of thisapproach as well as other recently published molecular phylogenies and phylogenomic inferencesTaking into account the progress that has been made in the last few years by analysing molecular andnon-molecular data a new synopsis of the suprageneric classification of the Bryophyta is presentedTaxonomic changes comprise a re-evaluation of the taxonomy of Takakia (including Takakiophytinastat nov) Gigaspermidae subclass nov elevation of subfamilies of Dicranaceae to family level(Amphidiaceae stat nov Dicranellaceae stat nov Oncophoraceae stat nov) Hypodontiaceae famnov and Helicophyllales ord nov

Key words Bryophyta suprageneric classification molecular phylogeny trnLUAA

intron atpB-rbcLspacer psbA-trnH spacer

Introduction

Mosses form the second largest of the major land plant lineages They compriseapproximately 12800 species (Crosby et al 1999) and exhibit a high morphologicaland ecological diversity Traditionally the three groups of bryophytes (mossesliverworts and hornworts) were treated as classes of the division Bryophyta Moleculardata however revealed that bryophytes are paraphyletic with liverworts being sisterto all other extant land plants and mosses sister to a clade of hornworts and vascularplants (Qiu et al 2006) As the three bryophyte groups obviously represent independentlineages in land plant evolution it is now widely accepted to treat them as separatedivisions Bryophyta (mosses) Marchantiophyta (liverworts) and Anthocerotophyta

2

(hornworts) In contrast to the latter two groups mosses are scarcely characterisedin terms of morphological-anatomical synapomorphies At the molecular levelhowever all three bryophyte lineages are well circumscribed (eg Qiu et al 1998Stech et al 2003 Cox et al 2004 Shaw amp Renzaglia 2004 Groth-Malonek et al2005 Forrest et al 2006 Qiu et al 2006) A general overview of the present state ofbryophyte phylogeny was recently provided by Renzaglia et al (2007)

In the 19th and 20th century different and often contradictory classification systemsof mosses were published which either relied more on gametophytic or on sporophyticcharacters (summarised for example in Buck 2007) Nowadays the phylogeneticsignificance of morphological-anatomical characters can be evaluated based onmolecular phylogenies The most recent classifications of liverworts (Frey amp Stech2005 He-Nygreacuten et al 2006) hornworts (Stotler amp Crandall-Stotler 2005 Duff etal 2007) and mosses (Goffinet amp Buck 2004) already integrated molecular and non-molecular characters to provide a consensus of the current knowledge Howeverseveral suprageneric relationships within the mosses remained unresolved orambiguous at the time of the Goffinet amp Buck (2004) classification such as ordinalrelationships within the Bryidae and the closest relatives of pleurocarpous mossesA number of recent attempts shed more light on these problematic relationships(eg Tsubota et al 2004 Shaw et al 2005 Stech amp Quandt 2006 Bell et al 2007Goffinet et al 2007 contributions in Newton amp Tangney 2007 Quandt et al 2007this paper) Although some clades of the moss phylogeny are still partly contradictoryor do not receive significant statistical support these studies seem to converge on acommon hypothesis of moss relationship at suprageneric levels allowing us toestablish an updated and revised classification

In the present study a molecular phylogeny of the Bryopsida is presented based on anew approach ie the combined analysis of solely non-coding plastid markers (trnL

UAAintron atpB-rbcL spacer psbA-trnH spacer) The current state of moss systematicsis discussed with respect to the impact of this approach as well as recently publishedmolecular phylogenies and phylogenomic inferences Finally we propose a newsynopsis of the suprageneric classification of the Bryophyta which updates that ofGoffinet amp Buck (2004) A detailed description of the taxa down to genus level willbe provided by a forthcoming new edition of Englers Syllabus of Plant Familiesfor which additional taxonomic changes are made here

Material and methods

TAXON SAMPLING A molecular data set of 85 species of Bryopsida was assembled by compilingsequences from own previous analyses and by sequencing of herbarium material Voucher informationand GenBank accession numbers are summarised in Table 1 together with indications of the newlysequenced accessions From 21 species all three non-coding markers employed here were newlysequenced In few cases sequences available in GenBank were used to complete the data set Andreaearupestris Hedw (Andreaeopsida) and Pogonatum subulatum (Menzies ex Brid) Brid (Poly-trichopsida) were used as outgroup representatives

DNA EXTRACTION PCR AND SEQUENCING DNA was extracted using the mixer mill MM200 (Retsch)and following the method of Doyle amp Doyle (1990) PCR reactions for trnL intron and atpB-rbcLspacer followed the protocols given in Frey et al (1999) and Stech (2004) and were performed with

3

Tab

le 1

Vou

cher

info

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and

Gen

Ban

k ac

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num

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of t

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for t

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nced

for

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Fam

ilyS

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Acc

no

Acc

no

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aea

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4297

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3128

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Tab

le 1

con

tinu

ed

6

primers CM

DM

(slightly modified after Taberlet et al 1991 see Frey et al 1999) and atpB-1rbcL-1(Chiang et al 1998) respectively For amplification of the psbA-trnH spacer primers psbAF(5-GTT ATG CAT GAA CGT AAT GCT C-3 Sang et al 1997) and trnHR-2 (5-CGC GCA TGGTGG ATT CAC AAT CC-3 slightly modified after Sang et al 1997) were used with a PCRprotocol of 5 min 94degC 35 cycles (30 sec 94degC 1 min 48degC 1 min 40 sec 72degC) 7 min 72degC PCRproducts were purified using DNA purification kits (Qiagen Macherey-Nagel) Sequencing wasperformed as described in Stech (2004) using the amplification primers

ALIGNMENT AND PHYLOGENETIC ANALYSES DNA sequences were manually aligned in PhyDE v0992(Muumlller et al 2005) Following Quandt et al (2003) and Quandt amp Stech (2005) inversions inputative hairpin secondary structures were positionally separated in the alignment their presence orabsence was not coded for the phylogenetic analyses Phylogenetic reconstructions under the maximumparsimony criterion were performed using winPAUP 40b10 (Swofford 2002) in combination withPRAP (Muumlller 2004) as implemented in SeqState (Muumlller 2005) PRAP generates command filesfor PAUP that allow parsimony ratchet searches as designed by Nixon (1999) Heuristic searchesunder parsimony were performed with the following options all characters equally weighted andunordered TBR branch swapping collapse branches if maximum branch length is zero MulTreesoption in effect gaps treated as missing data Initially a heuristic search with 1000 addition sequencereplicates was performed For the parsimony ratchet ten random addition cycles of 200 ratchetiterations each were used with TBR branch swapping on a randomly re-weighted data set (25 ofthe positions) Heuristic bootstrap searches were performed with 1000 replicates with 10 additionsequence replicates per bootstrap replicate

Results

In the present data set of non-coding plastid markers sequence lengths ranged from243 to 368 nucleotides (nt) in the trnL intron and from 445 to 615 nt in the atpB-rbcL spacer The psbA-trnH spacer was considerably shorter than the other twomarkers and ranged from 103 to 186 nt The combined alignment of sequences from85 ingroup and two outgroup taxa comprised 2430 positions (trnL intron 668 atpB-rbcL spacer 1366 psbA-trnH spacer 396 positions) The most variable regions withambiguous alignment (781 positions) were excluded from phylogenetic analysis Ofthe 1649 included positions 628 (381) were variable and 455 of the variablepositions (725 or 276 of the total number of positions) were parsimony-informative The trnL intron comprised 124 the atpB-rbcL spacer 286 and the psbA-trnH spacer 45 of these included parsimony-informative positions

The shortest trees found in the heuristic maximum parsimony analysis of the combineddata set had a length of 2433 steps By applying the parsimony ratchet 129 treeswere retained that were one step shorter (length 2432 CI = 0419 RI = 0624) Thestrict consensus tree of the ratchet analysis is shown in Fig 1 The ingroup (Bryopsida)is supported with 100 bootstrap support (BS) Diphysciidae are sister to theremaining Bryopsida with 54 BS Encalyptidae Funariidae Timmiidae andDicranidae all receive gt 95 BS while Bryidae are slightly less supported (89BS) Relationships between these major lineages are resolved but unsupported Atordinal level within the Bryidae a lower resolution is observed SplachnalesOrthotrichales Aulacomniales Hypnodendrales Hookeriales and Hypnales areresolved as monophyletic with 67-100 BS whereas Hedwigiales BartramialesBryales Orthodontiales and Rhizogoniales are not A closer relationship ofOrthotrichales with the pleurocarpous mosses sl than with the more basal ordersHedwigiales Bartramiales Splachnales and Bryales is indicated

7

Discussion

Classification of mosses - recent progress and the current state

For a long time mosses were subdivided into three main lineages the subclassesSphagnidae Andreaeidae and Bryidae (eg Fleischer 1920 Vitt 1984 Frahm ampFrey 1987) the latter with a number of (super-)orders (eg Frey 1977) Howevermolecular data confirmed that mosses comprise a number of isolated basal lineagesrepresented by morphologically and ecologically distinct extant taxa such as TakakiaSphagnum Andreaea Andreaeobryum Oedipodium Tetraphis the Polytrichaceaeand Buxbaumia which probably have long independent phylogenetic histories (cfNewton et al 2007) As a result of molecular phylogenies and a re-evaluation ofmorphological-anatomical characters the classification of mosses has changedconsiderably in the last few years with the main lineages nowadays treated atsubdivision class and subclass levels within division Bryophyta (eg Doweld 2001Ochyra et al 2003 Goffinet amp Buck 2004 this study)

Takakia and Sphagnum are the earliest diverging moss taxa in molecular phylogenies(eg Newton et al 2000 Beckert et al 2001 Cox et al 2004 Qiu et al 2006Newton et al 2007) That Takakia is a moss and not a liverwort was confirmed byanalysis of DNA sequences and phylogenomic characters such as the distribution ofmitochondrial introns (eg Beckert et al 2001) Its taxonomic status however stillremains to be clarified On the one hand most molecular studies resolve Takakiaand Sphagnum as sister genera although only partly with high statistical supportThese molecular topologies do not support the recognition of division Takakiophytaas proposed by Crandall-Stotler (1986) One the other hand no morphologicalsynapomorphies unite Takakia with Sphagnum and significant molecular differencesseparating Takakia from all other mosses were also observed For example a regionin the plastid ITS3 is similar to that of other land plants but absent in mosses(Samigullin et al 2002) and a transition in the trnL

UAA gene changing the anticodon

to CAA was otherwise only found in leptosporangiate ferns and Ginkgo (Quandt etal 2004) Thus ldquoresolution of Sphagnum - Takakia clade may be an artifactrdquo (Shawamp Renzaglia 2004) Also Goffinet amp Buck (2004) did not unite Takakia and Sphagnumunder a formal taxonomic rank but placed them into different informal superclassesIn our opinion Takakia should be treated at the same level as Sphagnophytina andBryophytina (cf Doweld 2001) ie as a subdivision of Bryophyta However morefundamental nomenclatural changes are necessary as the family name Takakiaceaewas not validated in the original publication by Hattori amp Inoue (1958) (article411 of ICBN McNeill et al 2006) and consequently all higher taxa erected laterare invalid The corrected taxonomic treatment of Takakia is provided here withsporophytic characters included in the latin diagnosis of Takakiaceae (see taxonomy)

Within Bryophytina we recognise four morphologically and molecularly isolatedbasal lineages as separated from the arthrodontous mosses (Bryopsida) Andreaeopsida(with linear capsule dehiscence) the operculate but eperistomate Oedipodiopsida aswell as Polytrichopsida and Tetraphidopsida with nematodontous peristomes A fifthclass Andreaeobryopsida was erected by Buck amp Goffinet (2000) but re-includedin Andreaeopsida as a subclass by Ochyra et al (2003) The systematic status of

8

Andreaeobryum macrosporum Steere amp BMMurray and possible relationships withAndreaea and Takakia were discussed by Murray (1988) and summarised includingmolecular results by Shaw amp Renzaglia (2004)

On the next lower level a number of morphologically and molecularly divergentlineages are nowadays treated as subclasses of Bryopsida Buxbaumiidae andDiphysciidae are generally branching off first in molecular topologies (eg Beckertet al 2001 Magombo 2003 Cox et al 2004) followed by Timmiidae Encalyptidaeand Funariidae as well as Dicranidae (haplolepideous mosses) sister to Bryidae slThese subclasses (except Buxbaumiidae not included) are also well recognizable inthe present analysis of non-coding plastid sequences (Fig 1)

The morphologically very different Encalyptidae and Funariidae are revealed assister groups although mostly without high support in several molecular phylogenies(eg Goffinet et al 2001 Cox et al 2004 Hedderson et al 2004 Tsubota et al2003 2004) and also in the present study (Fig 1) Goffinet et al (2007) confirmedthis relationship by phylogenomic evidence namely a large (71 kb) inversion in thechloroplast genome of Funariaceae Disceliaceae and Encalyptaceae but not inGigaspermaceae Consequently the latter family was separated at ordinal level fromthe two remaining families of Funariales by Goffinet et al (2007) GigaspermalesFunariales and Encalyptales may share a common ancestor according to some butnot all molecular phylogenies (eg Goffinet et al 2001 2007 Hedderson et al2004 but not in Tsubota et al 2004) Although ontogenetic data from peristomedevelopment may support their common ancestry (Goffinet et al 2007) unambiguousmorphological synapomorphies are lacking We therefore propose to treatGigaspermaceae at subclass level within the Bryopsida (see taxonomy)

The haplolepideous mosses (Dicranidae) are clearly supported as a monophyleticlineage which obviously evolved from a diplolepideous ancestor according to theirposition in the molecular trees (eg Newton et al 2000 Tsubota et al 2003 Cox etal 2004 Goffinet amp Buck 2004) Molecular studies suitable for inferring ordinaland family level relationships within Dicranidae either focused on the haplolepideousmosses (eg Stech 1999ab 2004 LaFarge et al 2000 2002 Tsubota et al 2003Hedderson et al 2004) or included more than 15 haplolepideous taxa in analyses ofa broader range of mosses (eg Goffinet et al 2001 Tsubota et al 2004 this study)Major lineages supported by these analyses are for example Grimmiales(Grimmiaceae Ptychomitriaceae and Seligeriaceae) Leucobryaceae (incl formerDicranaceae-Campylopoideae and Paraleucobryoideae pp) Dicranaceae sstr(Dicranoideae plus former Dicnemonaceae and Paraleucobryoideae pp) Pottiaceae(incl Cinclidotaceae and Splachnobryum) and Calymperaceae (probably exclOctoblepharum) Furthermore several genera and families belong to Dicranidaewhose systematic positions have been controversial (eg Stech et al 1999b LaFarge et al 2002 Hedderson et al 2004 OBrien 2007 Quandt et al 2007 thisstudy) Amphidium Archidium Catoscopium Drummondia EphemeraceaeErpodiaceae Mittenia (cf OBrien 2007 sequences in some earlier analyses werebased on misdentified specimens) Rhachitheciaceae Schistostega Splachnobryumand Wardia On the contrary several problems remain such as the circumscriptionof Ditrichaceae and relationships of the major haplolepideous lineages in general

9

Fig 1 Strict consensus tree of 129 most parsimonious trees inferred from combined trnLUAA

intronatpB-rbcL spacer and psbA-trnH spacer sequences of 85 taxa of Bryopsida as well as Andreaearupestris (Andreaeopsida) and Pogonatum subulatum (Polytrichopsida) as outgroup representativesBootstrap support values gt50 are depicted above the branches

10

Consequently resolving the phylogeny of Dicranidae with confidence is one of themajor future challenges in moss systematics

As mentioned above Dicranaceae are monophyletic in a narrow circumscriptionaccording to molecular data In contrast to former Campylopoideae andParaleucobryoideae the status of Rhabdoweisioideae (= Oncophoroideae Ochyra2002) and Dicranelloideae needs further consideration Stech (1999ab) suggestedto recognise RhabdoweisioideaeRhabdoweisiaceae in a broad sense includingDicranoweisia Amphidium and Aongstroemia Subsequent molecular analysesconfirmed a close relationship of the genera Arctoa Cynodontium DicranoweisiaKiaeria Oncophorus Oreoweisia Oreas Rhabdoweisia and Symblepharis althoughwithout significant support (La Farge et al 2002 Tsubota et al 2003 Hedderson etal 2004) With respect to the molecular evidence available so far we propose toelevate Oncophoroideae to family level to accomodate these genera and perhapsGlyphomitrium (cf Tsubota et al 2003) whereas we consider AongstroemiaDichodontium and Diobelonella to belong to Aongstroemiaceae (cf Stech 1999a)Amphidium is neither closely related to Dicranaceae sstr nor to Oncophoroideae(La Farge et al 2002 Tsubota et al 2003 Hedderson et al 2004 Stech 2004 thisstudy) and should be treated at family level rather than placed in Dicranaceae assubfam Amphidioideae (Ochyra et al 2003) The circumscription of Dicranelloideaeis more difficult to evaluate as few representatives have been included in molecularanalyses However Dicranella heteromalla (Hedw) Schimp as well as the generaCampylopodium and Microcampylopus are clearly separated from Dicranaceae sstr(Stech 1999a 2004 La Farge et al 2002 Tsubota et al 2003 Hedderson et al2004) and consequently the subfamily deserves family status as well Finallymolecular data showed that the genus Hypodontium does not belong to Pottiaceae(Hedderson et al 2004 Tsubota et al 2004) Taxonomic conclusions have not beendrawn from these results which is made up here (see taxonomy)

All mosses with diplolepideous-alternate peristomes together with Splachnales witha diplolepideous-opposite (Funaria-type) peristome form a monophyletic group inmolecular analyses (eg Newton et al 2000 Beckert et al 2001 Goffinet et al2001 Cox et al 2004 Tsubota et al 2004 references in Table 2) Differentclassifications of this by far most species-rich group of mosses were proposed (egVitt et al 1998 Ochyra et al 2003 Goffinet amp Buck 2004) However at least someof the recognised subclasses and superorders are paraphyletic according to themolecular topologies and assigning formal ranks to all evolutionarily significantmonophyletic entities is problematic if the main taxonomic framework of Bryophytaand Bryopsida should be maintained (cf discussion in Bell et al 2007) Thereforein the present synopsis only one subclass Bryidae is recognised for all diplolepideous-alternate mosses and Splachnales This broadly defined Bryidae is subdivided into13 orders most of them resolved as monophyletic in the majority of the phylogeneticanalyses summarised in Table 2 although with different levels of statistical supportin maximum parsimony analyses To define monophyletic lineages at supraordinallevel informal node-based names may be chosen according to Bell et al (2007) Forexample the pleurocarpous mosses (pleurocarpy sensu Bell amp Newton 2007) andtheir closest acrocarpous relatives (Orthodontiales to Hypnales) were already

11

Table 2 Taxon sampling and bootstrap support (BS) for Dicranidae Bryidae and orders within theBryidae in recent phylogenetic analyses (MP only) based on combined molecular markers Markersare given in square brackets (non-coding regions in bold) numbers of included taxa in brackets ++respective clade present with ge 80 BS + clade present with lt 80 BS - clade not present no oronly one representative included

Bell amp Newton OBrien Quandt et al Bell et al this study(2004) (2007) (2007) (2007)

[rbcL rps4 [atpB atpB- [rbcL rps4 [rbcL rps4 [atpB-rbcLnad5] rbcL rbcL trnL-F nad5] trnL-F nad5] psbA-trnH

rps4 trnL-F] trnL]

Dicranidae + (2) + (4) ++ (3) (1) ++ (19)Bryidae ++ (57) + (53) ++ (52) ++ (98) ++ (58)Hedwigiales ++ (2) (1) ++ (2) ++ (2) - (3)Bartramiales ++ (2) ++ (4) ++ (4) ++ (3) - (4)Splachnales (0) ++ (2) ++ (3) ++ (2) ++ (5)Bryales - (4) - (5) ++ (18) + (17) - (8)Orthotrichales (1) ++ (3) ++ (3) ++ (2) ++ (4)Orthodontiales + (4) + (4) + (3) + (6) - (3)Aulacomniales + (6) + (7) ++ (2) + (7) + (3)Rhizogoniales ++ (13) + (8) ++ (5) ++ (14) - (3)Hypnodendrales ++ (13) + (7) ++ (4) ++ (29) ++ (6)Ptychomniales ++ (3) ++ (3) (1) ++ (4) (1)Hookeriales - (4) + (2) (1) + (2) + (8)Hypnales - (5) - (7) ++ (5) ++ (10) + (10)

summarised under the informal node based name pleurcarpids (Bell et al 2007)and can be distinguished from a basal grade of acrocarpous or cladocarpous lineages(Hedwigiales to Orthotrichales) Within the latter monophyly of BartramialesSplachnales and Orthotrichales is well-supported in all analyses including two ormore taxa except Bartramiales in the present data set (cf Fig 1) In contrast Bryalesreceive significant support less frequently (but see Bell et al 2007 Quandt et al2007) Hedwigiales are well supported if only Hedwigia (Hedwigiaceae) andRhacocarpus (Rhacocarpaceae) are included whereas the monospecific Helicophyllum(Helicophyllaceae) is not closely related to these taxa but shows affinities withBartramiales (Goffinet et al 2001 this study) With respect to the differentmorphologies of Helicophyllaceae and Bartramiaceae however the former shouldbe separated at ordinal level (see taxonomy)

Clarifying relationships of the Orthotrichales is still a difficult issue Analyses ofsingle chloroplast markers or parsimony analyses of combined markers from differentgenomes mostly indicated a close relationship either with Splachnales (eg Cox etal 2000 Newton et al 2000 Tsubota et al 2004 Quandt et al 2007) or with thepleurocarpids (Goffinet et al 2001 this study) Although none of these alternativesis well-supported the latter seems more likely with regard to the moderately tomaximally supported Orthotrichales - pleurocarpid sister group relationship in allanalyses of mitochondrial data and in likelihood analyses of combined plastidmitochondrial markers (Beckert et al 2001 Quandt et al 2007)

12

The molecular polyphyly of Rhizogoniaceae (eg Bell amp Newton 2004) was solvedby the transfer of rhizogonioid genera into broadly defined Aulacomniaceae andOrthodontiaceae (Bell et al 2007) which now include both acrocarpous andpleurocarpous taxa These systematic changes are also comprehensible by non-molecular characters such as morphological traits shared by Mesochaete andAulacomnium heterostichum (Hedw) Bruch amp Schimp or the variously reducedperistomes of Orthodontiaceae pp in contrast to the generally fully developed Bryum-type peristomes of rhizogonioid and hypnodendroid mosses (Bell et al 2007) Theposition of the solely pleurocarpous Hypnodendrales sister to the former Hypnidaeled to the recognition of the informal group core pleurocarps (Bell et al 2007)The former Hypnidae (Ptychomniales Hookeriales and Hypnales summarised ashomocostate pleurocarps) are monophyletic in most molecular analyses (eg Goffinetet al 2001 Tsubota et al 2004 Bell et al 2007) with Ptychomniales being well-supported (Pedersen amp Newton 2007 Table 2) Clarifying relationships betweenHookeriales and Hypnales and within the latter is still a challenge but recent molecularstudies seem to support a sister group relationship of both orders (Bell et al 2007present study)

Phylogenetic utility of non-coding plastid markers

Non-coding plastid markers that comprise both variable and conserved regionssuch as the trnL

UAA intron have repeatedly been shown to possess potential for

resolving relationships at high taxonomic levels (eg Borsch et al 2003 Quandtet al 2004) Both the trnL intron and atpB-rbcL spacer were characterised indetail in mosses with respect to their structure and molecular evolution (Quandt ampStech 2005 Stech amp Quandt 2006) They include conservative regions that can beunambiguosly aligned and even parts of the more variable regions can be used ifrepeats hairpin loops etc are correctly identified and adequately treated in thephylogenetic analyses (eg Quandt et al 2003 Quandt amp Stech 2005) Using theatpB-rbcL spacer alone (Stech amp Quandt 2006) relationships of the major mosslineages were largely consistent with the ldquototal evidencerdquo molecular tree of Goffinetamp Buck (2004) However in addition to general limitations that result from singlemarker analyses the use of non-coding markers may pose further problems suchas a high amount of homoplasy resulting in low resolution or low statistical supportfor many clades Therefore several recent molecular studies of relationships withinBryidae have employed both coding and non-coding markers (Table 2)Nevertheless the usefulness of analyses of combined non-coding plastid markerscannot be ruled out In fact Fig 1 and Table 2 indicate a phylogenetic signal inthe present data set as many clades are recovered that are usually also resolvedin analyses of coding or combined coding and non-coding markers Especiallywith regard to statistical support however the present analysis is inferior tothose of other recent data sets especially Bell et al (2007) and Quandt et al(2007) In addition the non-coding markers used here are of different suitabilityand even the two intergenic spacers differ considerably from each other ThepsbA-trnH spacer contributes much less to the trees resolution than the atpB-rbcL spacer first because it is much shorter and second because relatively largeparts are attributed to hairpin loops or otherwise hypervariable regions These

13

results indicate that future studies should evaluate the molecular evolution andphylogenetic potential of new markers both coding and con-coding and choosethe most suitable ones in a combined analysis to resolve the remaining uncertaintiesin moss phylogeny

Taxonomy

Takakiaceae Stech amp WFrey stat nov

Plantae virides nusquam rhizophorae sine protonemate e caudicis rhizomatis erectae Caudicesrhizomati et axes geotropi radiformes frequenter intercalariter ramificantes sine phyllidiis cumpapillis mucilaginis rostratis Caules phyllidiiferi saepe furcati Phyllidia sine lamina et costadistincta profunde 2-4(-5)-lobata pluristratosa tristicha sed torsione spiraliter disposita Filumcentralium in ambabus generationibus (axibus gametophyti et setis) adest Plantae dioicae Antheridiaet archegonia nuda Sporophytum terminale solitarium Seta persistens Capsula tortilis admaturitatem schizocarpa secus unam rimam spiralem longitudinalem dehiscens Stomata etoperculum absunt peristomium nullum Calyptra mitriformis

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiaceae SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval (Art 411)

Takakiales Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiales SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval

Takakiales SHatt amp Inoue ex RMSchust J Hattori Bot Lab 26 224 1963 nom inval (cumdescr latin)

Takakiopsida Stech amp WFrey statnov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiopsida Goffinet amp WRBuck Monogr Syst Bot Missouri Bot Gard 98 232 2004 nominval

Takakiopsida Jia et al Acta Phytotax Sin 41 350 351 2003 nom nud

Takakiopsida Wang amp Wu Fl Bryophyt Sin 8 447 2004 nom inval (cum descr latin)

Takakiophytina Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue JHattori Bot Lab 19 137 1958

Gigaspermidae Stech amp WFrey subclass nov

Plantae acrocarpae terrestres stoloniferae ramis brevibus erectis Folia unicostata cellulis laxislaevibus Capsula plerumque valde rugosa gymnostomatica vel cleistocarpa stomata cum duabuscellulis sociis Ab Funariidis et Encalyptidis charactere phylogenomico (71-kb inversio abest)separatae

14

TYPUS Gigaspermum Lindb Oumlfversigt af Foumlrhandlingar Kongl Svenska Vetenskaps-Akademien21 599 1865

Amphidiaceae Stech stat nov

Based on Dicranaceae subfam Amphidioideae Ochyra in Ochyra Zarnowiec amp Bednarek-OchyraCens Cat Polish Mosses 110 2003

TYPUS Amphidium Schimp Coroll Bryol Eur 39 1856

Amphidiaceae AJESm Moss Fl Britain Ireland 2nd ed 657 2004 nom inval descr angl

Dicranellaceae Stech stat nov

Based on Dicranaceae subfam Dicranelloideae Lindb Utkast Eur Bladmoss 33 1878[lsquoUnderfamilje Dicranelleaersquo]

TYPUS Dicranella (MuumlllHal) Schimp Coroll Bryol Eur 13 1856

Oncophoraceae Stech stat nov

Based on Dicranaceae subfam Oncophoroideae Lindb Utkast Eur Bladmoss 34 1878[lsquoUnderfamilje Oncophoreaersquo]

TYPUS Oncophorus (Brid) Brid Bryol Univ 1 389 1826

Hypodontiaceae Stech fam nov

Plantae robustae characteribus morphologicis Pottiaceis et Calymperaceis similes sedcharacteribus molecularicis separatae Bracteae perichaetiales internae e basi vaginantes subulataevel aristatae Capsula aspectu succulenta cellulae exothecii incrassatae annulus magnopereabsens Peristomii dentes breves triangulati incurvati aurantiaci leves vel infirme verrucosiCalyptra cucullata

TYPUS Hypodontium MuumlllHal Hedwigia 38 96 1899

Helicophyllales Stech amp WFrey ord nov

Plantae acrocarpae prostratae tomentosae Folia dimorpha in duas series laterales et unam seriemventralem divisa Costa percurrens Cellulae hexagonae ad subquadratae papillosae Capsula immersacupulata ad oblonga infra orificium abrupte incurvata stomata destituta Peristomium nullum Sporaeisomorphae heteropolares granulatae

TYPUS Helicophyllum Brid Bryol Univ 2 771 1827

Synopsis of the suprageneric classification of BryophytaAuthor citations are in accordance with Art 492 of the Vienna Code (McNeill et al 2006)

Subdivision Takakiophytina Stech amp WFreyClass Takakiopsida Stech amp WFrey

Order Takakiales Stech amp WFreyTakakiaceae Stech amp WFrey

Subdivision Sphagnophytina DoweldClass Sphagnopsida Schimp

Order Sphagnales Limpr

15

Sphagnaceae DumortOrder Ambuchananiales Seppelt amp HACrum

Ambuchananiaceae Seppelt amp HACrumSubdivision Bryophytina Engler

Class Andreaeopsida JHSchaffnSubclass Andreaeidae Engl

Order Andreaeales LimprAndreaeaceae Dumort

Subclass Andreaeobryidae OchyraOrder Andreaeobryales BMMurray

Andreaeobryaceae Steere amp BMMurrayClass Oedipodiopsida Goffinet amp WRBuck

Order Oedipodiales Goffinet amp WRBuckOedipodiaceae Schimp

Class Tetraphidopsida Goffinet amp WRBuckOrder Tetraphidales MFleisch

Tetraphidaceae SchimpClass Polytrichopsida Doweld

Order Polytrichales MFleischPolytrichaceae Schwaumlgr

Class Bryopsida PaxSubclass Buxbaumiidae Doweld

Order Buxbaumiales MFleischBuxbaumiaceae Schimp

Subclass Diphysciidae OchyraOrder Diphysciales MFleisch

Diphysciaceae MFleischSubclass Timmiidae Ochyra

Order Timmiales OchyraTimmiaceae Schimp

Subclass Encalyptidae Ochyra Żarnowiec amp Bednarek-OchyraOrder Encalyptales Dixon

Encalyptaceae SchimpSubclass Funariidae Ochyra

Order Funariales MFleischFunariaceae Schwaumlgr Disceliaceae Schimp

Subclass Gigaspermidae Stech amp WFreyOrder Gigaspermales Goffinet Wickett OWerner Ros AJShaw amp CJCox

Gigaspermaceae LindbSubclass Dicranidae Doweld

Order Catoscopiales Ignatov amp IgnatovaCatoscopiaceae Broth

Order Scouleriales Goffinet amp WRBuckDrummondiaceae Goffinet Scouleriaceae SPChurchill

Order Bryoxiphiales HACrum amp LEAndersonBryoxiphiaceae Besch

16

Order Grimmiales MFleischGrimmiaceae Arn Ptychomitriaceae Schimp Seligeriaceae Schimp

Order Archidiales LimprArchidiaceae Schimp

Order Mitteniales ShawMitteniaceae Broth

Order Dicranales HPhilib ex MFleischAmphidiaceae Stech Aongstroemiaceae De Not BruchiaceaeSchimp Calymperaceae Kindb Dicranaceae Schimp Dicranel-laceae Stech Ditrichaceae Limpr Erpodiaceae Broth EustichiaceaeBroth Fissidentaceae Schimp Leucobryaceae Schimp Onco-phoraceae Stech Rhachitheciaceae HRob Schistostegaceae SchimpViridivelleraceae IGStone Wardiaceae Welch

Order Pottiales MFleischEphemeraceae Schimp Hypodontiaceae Stech PleurophascaceaeBroth Pottiaceae Schimp Serpotortellaceae WDReese amp RHZander

Subclass Bryidae EnglOrder Hedwigiales Ochyra

Hedwigiaceae Schimp Rhacocarpaceae KindbOrder Helicophyllales Stech amp WFrey

Helicophyllaceae BrothOrder Bartramiales DQuandt NEBell amp Stech

Bartramiaceae SchwaumlgrOrder Splachnales Ochyra

Meesiaceae Schimp Splachnaceae Grev amp ArnOrder Bryales Limpr

Bryaceae Schwaumlgr Leptostomataceae Schwaumlgr Mniaceae SchwaumlgrPhyllodrepaniaceae Crosby Pseudoditrichaceae Steere amp ZIwatsPulchrinodaceae DQuandt NEBell amp Stech

Order Orthotrichales DixonOrthotrichaceae Arn

Order Orthodontiales NEBell AENewton amp DQuandtOrthodontiaceae Goffinet

Order Aulacomniales NEBell AENewton amp DQuandtAulacomniaceae Schimp

Order Rhizogoniales Goffinet amp WRBuckRhizogoniaceae Broth

Order Hypnodendrales NEBell AENewton amp DQuandtBraithwaiteaceae NEBell AENewton amp DQuandt Hypnodendra-ceae Broth Pterobryellaceae WRBuck amp Vitt Racopilaceae Kindb

Order Ptychomniales WRBuck CJCox AJShaw amp GoffinetPtychomniaceae MFleisch

Order Hookeriales MFleischDaltoniaceae Schimp Hookeriaceae Schimp HypopterygiaceaeMitt Leucomiaceae Broth Pilotrichaceae Kindb SaulomataceaeWRBuck CJCox AJShaw amp Goffinet Schimperobryaceae WR

17

Buck CJCox AJShaw amp GoffinetOrder Hypnales WRBuck amp Vitt

Amblystegiaceae GRoth Anomodontaceae Kindb BrachytheciaceaeSchimp Calliergonaceae Vanderpoorten Hedenaumls CJCox amp AJShaw Catagoniaceae WRBuck amp Ireland Climaciaceae KindbCryphaeaceae Schimp Echinodiaceae Broth Entodontaceae KindbFabroniaceae Schimp Fontinalaceae Schimp Helodiaceae OchyraHeterocladiaceae Ignatov amp Ignatova Hylocomiaceae MFleischHypnaceae Schimp Lembophyllaceae Broth LeptodontaceaeSchimp Lepyrodontaceae Broth Leskeaceae Schimp Leucodon-taceae Schimp Meteoriaceae Kindb Microtheciellaceae HAMillamp AJHarr Myriniaceae Schimp Myuriaceae MFleisch NeckeraceaeSchimp Orthorrhynchiaceae SHLin Phyllogoniaceae KindbPlagiotheciaceae MFleisch Pleuroziopsidaceae Ireland Prionodon-taceae Broth Pseudoleskeaceae Schimp PseudoleskeellaceaeIgnatov amp Ignatova Pterigynandraceae Schimp PterobryaceaeKindb Pylaisiaceae Schimp Pylaisiadelphaceae Goffinet amp WRBuck Regmatodontaceae Broth Rhytidiaceae Broth RigodiaceaeHACrum Rutenbergiaceae MFleisch Scorpidiaceae Ignatov ampIgnatova Sematophyllaceae Broth Sorapillaceae MFleisch Ste-reophyllaceae WRBuck amp Ireland Symphyodontaceae MFleischTheliaceae MFleisch Thuidiaceae Schimp TrachylomataceaeWRBuck amp Vitt

Acknowledgements

Sincere thanks are due to JLReveal (Ithaca) as well as WFPrudhomme van Reine and JFVeldkamp(Leiden) for comments and discussions about suprafamilial taxonomy to DQuandt (Dresden) for providingDNA from Rhacocarpus and Bartramiaceae species and to BGiesicke (Berlin) for technical assistance

References

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BELL NE amp AE NEWTON (2004) Systematic studies of non-hypnanaean pleurocarps establishinga phylogenetic framework for investigating the origins of pleurocarpy - In GOFFINET BV HOLLOWELL amp R MAGILL (eds) Molecular systematics of bryophytes Monogr Syst BotMissouri Bot Gard 98 290-319

BELL NE amp AE NEWTON (2007) Pleurocarpy in the Rhizogoniaceous grade - In NEWTONAE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolution SystematicsAssociation Special Volume Series 71 41-64

BELL NE D QUANDT TJ OBRIEN amp AE NEWTON (2007) Taxonomy and phylogeny inthe earliest diverging pleurocarps square holes and bifurcating pegs - Bryologist 110 533-560

BORSCH T KW HILU D QUANDT V WILDE C NEINHUIS amp W BARTHLOTT(2003) Non-coding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms- J Evol Biol 16 558-576

18

BUCK WR (2007) The history of pleurocarp classification two steps forward one step back - InNEWTON AE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 1-18

BUCK WR amp B GOFFINET (2000) Morphology and classification of mosses - In SHAWAJ amp B GOFFINET (eds) Bryophyte Biology pp 71-123 Cambridge University PressCambridge

CHIANG TY BA SCHAAL amp CI PENG (1998) Universal primers for amplification andsequencing a noncoding spacer between atpB and rbcL genes of chloroplast DNA - Bot Bull AcadSin 39 245-250

COX CJ B GOFFINET AE NEWTON AJ SHAW amp TAJ HEDDERSON (2000)Phylogenetic relationships among the diplolepideous-alternate mosses (Bryidae) inferred from nuclearand chloroplast DNA sequences - Bryologist 103 224-241

COX CJ B GOFFINET AJ SHAW amp SB BOLES (2004) Phylogenetic relationships amongthe mosses based on heterogeneous Bayesian analysis of multiple genes from multiple genomiccompartments - Syst Bot 29 234-250

CRANDALL-STOTLER B (1986) Morphogenesis developmental anatomy and bryophytephylogenetics contra-indications of monophyly - J Bryol 14 1-23

CROSBY MR RE MAGILL B ALLEN amp S HE (1999) A checklist of the mosses - MissouriBotanical Garden St Louis Missouri

DOWELD A (2001) Prosyllabus Tracheophytorum - GEOS Moscow i-lxxx + 110 pp

DOYLE JJ amp JL DOYLE (1990) Isolation of plant DNA from fresh tissue - Focus 12 13-15

DUFF RJ JC VILLAREAL DC CARGILL amp KS RENZAGLIA (2007) Progress andchallenges towards developing a phylogeny and classification of the hornworts - Bryologist 110214-243

FLEISCHER M (1920) Natuumlrliches System der Laubmoose - Hedwigia 61 390-400

FORREST LL EC DAVIS DG LONG BJ CRANDALL-STOTLER A CLARK ampML HOLLINGSWORTH (2006) Unraveling the evolutionary history of the liverworts (Marchantio-phyta) multiple taxa genomes and analyses - Bryologist 109 303-334

FRAHM J-P amp W FREY (1987) Moosflora 2 Aufl - UTB 1250 Stuttgart

FREY W (1977) Neue Vorstellungen uumlber die Verwandtschaftsgruppen und die Stammesgeschichteder Laubmoose - In FREY W H HURKA amp F OBERWINKLER (Hrsg) Beitraumlge zur Biologieder Pflanzen pp 117-139 Stuttgart

FREY W amp M STECH (2005) A morpho-molecular classification of the liverworts (Hepa-ticophytina Bryophyta) - Nova Hedwigia 81 55-78

FREY W M STECH amp K MEIszligNER (1999) Chloroplast DNA-relationship in palaeoaustralLopidium concinnum (Hypopterygiaceae Musci) An example of steno-evolution in mosses Studiesin austral temperate rain forest bryophytes 2 - Plant Syst Evol 218 67-75

GOFFINET B amp WR BUCK (2004) Systematics of Bryophyta (mosses) from molecules to arevised classification - In GOFFINET B V HOLLOWELL amp R MAGILL (eds) Molecularsystematics of bryophytes Monogr Syst Bot Missouri Bot Gard 98 205-239

GOFFINET B CJ COX AJ SHAW amp TAJ HEDDERSON (2001) The Bryophyta (mosses)Systematic and evolutionary inferences from an rps4 gene (cpDNA) phylogeny - Ann Bot 87191-208

GOFFINET B NJ WICKETT O WERNER RM ROS AJ SHAW amp CJ COX (2007)Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae(Bryophyta) - Ann Bot 99 747-753

19

GROTH-MALONEK M D PRUCHNER F GREWE amp V KNOOP (2005) Ancestors oftrans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosseswith vascular plants - Mol Biol Evol 22 117-125

HATTORI S amp H INOUE (1958) Preliminary report on Takakia lepidozioides - J Hattori BotLab 19 133-137

HE-NYGREacuteN X A JUSLEacuteN I AHONEN D GLENNY amp S PIIPPO (2006) Illuminating theevolutionary history of liverworts (Marchantiophyta) - towards a natural classification - Cladistics22 1-31

HEDDERSON TAJ DJ MURRAY CJ COX amp TL NOWELL (2004) Phylogeneticrelationships of haplolepideous mosses (Dicranidae) inferred from rps4 gene sequences - Syst Bot29 29-41

LA FARGE C BD MISHER JA WHEELER DP WALL K JOHANNES S SCHAFFERamp AJ SHAW (2000) Phylogenetic relationships within the haplolepideous mosses - Bryologist103 257-276

LA FARGE C AJ SHAW amp DH VITT (2002) The circumscription of the Dicranaceae(Bryopsida) based on the chloroplast regions trnL-trnF and rps4 - Syst Bot 27 435-452

MAGOMBO ZLK (2003) The phylogeny of basal peristomate mosses evidence from cpDNAand implications for peristome evolution - Syst Bot 28 24-38

MCNEILL J FR BARRIE HM BURDET V DEMOULIN DL HAWKSWORTHK MARHOLD DH NICOLSON J PRADO PC SILVA JE SKOG JH WIERSEMA ampNJ TURLAND (2006) International Code of Botanical Nomenclature (Vienna Code) - RegnumVegetabile 146 1-568

MUumlLLER K (2004) PRAP - computation of Bremer support for large data sets - Mol PhylogenetEvol 31 780-782

MUumlLLER K (2005) SeqState - primer design and sequence statistics for phylogenetic DNA datasets - Appl Bioinformatics 4 65-69

MUumlLLER K D QUANDT J MUumlLLER amp C NEINHUIS (2005) PhyDE v0992 PhylogeneticData Editor - httpwwwphydede

MURRAY BM (1988) Systematics of the Andreaeopsida (Bryophyta) two orders with links toTakakia - Nova Hedwigia Beih 90 289-336

NEWTON AE amp RS TANGNEY (eds) (2007) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 CRC Press Boca Raton 434 pp

NEWTON AE CJ COX JG DUCKETT JA WHEELER B GOFFINET TAJ HEDDER-SON amp BD MISHLER (2000) Evolution of the major moss lineages Phylogenetic analyses basedon multiple gene sequences and morphology - Bryologist 103 187-211

NEWTON AE N WIKSTROumlM NE BELL LL FORREST amp MS IGNATOV (2007)Dating the diversification of the pleurocarpous mosses - In NEWTON AE amp RS TANGNEY(eds) Pleurocarpous mosses systematics and evolution Systematics Association Special VolumeSeries 71 337-366

NIXON KC (1999) The parsimony ratchet a new method for rapid parsimony analysis - Cladistics15 407-411

OBRIEN TJ (2007) The phylogenetic distribution of pleurocarpous mosses evidence fromcpDNA sequences - In NEWTON AE amp RS TANGNEY (eds) Pleurocarpous mossessystematics and evolution Systematics Association Special Volume Series 71 19-41

OCHYRA R (2002) Nomenclatural changes in subfamilies of the Dicranaceae - CryptogamieBryol 23 345-349

20

OCHYRA R J ŻARNOWIEC amp H BEDNAREK-OCHYRA (2003) Census catalogue ofPolish mosses - Biodiv Poland 3 1-372

PEDERSEN N amp AE NEWTON (2007) Phylogenetic and morphological studies within thePtychomniales with emphasis on the evolution of dwarf males - In NEWTON AE amp RSTANGNEY (eds) Pleurocarpous mosses systematics and evolution Systematics AssociationSpecial Volume Series 71 367-392

QUANDT D amp M STECH (2005) Molecular evolution and secondary structure of the chloroplasttrnL intron in bryophytes - Mol Phylogenet Evol 36 429-443

QUANDT D K MUumlLLER amp S HUTTUNEN (2003) Characterisation of the chloroplast DNApsbT-H region and the influence of dyad symmetrical elements on phylogenetic reconstructions -Plant Biol 5 400-410

QUANDT D K MUumlLLER M STECH W FREY KW HILU amp T BORSCH (2004) Molecularevolution of the chloroplast trnL-F-region in land plants - In GOFFINET B V HOLLOWELL ampR MAGILL (eds) Molecular systematics of bryophytes Monogr Syst Bot Missouri Bot Gard98 13-37

QUANDT D NE BELL amp M STECH (2007) Unravelling the knot the Pulchrinodaceae famnov (Bryales) - In KUumlRSCHNER H T PFEIFFER amp M STECH (eds) A Festschrift to Wolf-gang Frey - a scientists life between deserts and rain forests Nova Hedwigia Beih 131 21-39

QIU Y-L Y CHO JC COX amp JD PALMER (1998) The gain of three mitochondrial intronsidentifies liverworts as the earliest land plants - Nature 394 671-674

QIU Y-L L LI B WANG Z CHEN V KNOOP M GROTH-MALONEK O DOM-BROVSKA J LEE L KENT J REST GF ESTABROOK TA HENDRY DW TAYLORCM TESTA M AMBROS B CRANDALL-STOTLER J DUFF M STECH W FREYD QUANDT amp CC DAVIS (2006) The deepest divergences in land plants inferred fromphylogenomic evidence - Proc Natl Acad Sci USA 103 15511-15516

RENZAGLIA KS S SCHUETTE RJ DUFF R LIGRONE AJ SHAW BD MISHLER ampJG DUCKETT (2007) Bryophyte phylogeny Advancing the molecular and morphological frontiers- Bryologist 110 179-213

SAMIGULLIN TH SP YACENTYUK GV DEGTYARYEVA KM VALIEJO-ROMANVK BOBROVA I CAPESIUS WF MARTIN AV TROITSKY VR FILIN amp ASANTONOV (2002) Paraphyly of bryophytes and close relationships of hornworts and vascularplants inferred from analysis of chloroplast rDNA ITS (cpITS) sequences - Arctoa 11 31-43

SANG T DJ CRAWFORD amp TF STUESSY (1997) Chloroplast DNA phylogeny reticulateevolution and biogeography of Paeonia (Paeoniaceae) - Amer J Bot 84 1120-1136

SHAW AJ amp KS RENZAGLIA (2004) Phylogeny and diversification of bryophytes - AmerJ Bot 91 1557-1581

SHAW AJ CJ COX amp B GOFFINET (2005) Global patterns of moss diversity taxonomic andmolecular inferences - Taxon 54 337-352

STECH M (1999a) A reclassification of Dicranaceae (Bryopsida) based on non-coding cpDNAsequence data - J Hattori Bot Lab 86 137-159

STECH M (1999b) A molecular systematic contribution to the position of Amphidium Schimp(Rhabdoweisiaceae Bryopsida) - Nova Hedwigia 68 291-300

STECH M (2004) Supraspecific circumscription and classification of Campylopus Brid(Dicranaceae Bryopsida) based on molecular data - Syst Bot 29 817-824

STECH M amp D QUANDT (2006) Molecular evolution of the chloroplast atpB-rbcL spacer inbryophytes - In SHARMA AK amp A SHARMA (eds) Plant Genome Biodiversity and EvolutionVol 2 Part B pp 409-431 Science Publishers Enfield New Hampshire

21

STECH M D QUANDT amp W FREY (2003) Molecular circumscription of the hornworts(Antho-cerotophyta) based on the chloroplast DNA trnL-trnF region - J Plant Res 116 389-398

STOTLER RE amp B CRANDALL-STOTLER (2005) A revised classification of theAnthocerotophyta and a checklist of the hornworts of North America north of Mexico - Bryologist108 16-26

SWOFFORD DL (2002) PAUP Phylogenetic analysis using parsimony (and other methods)version 40b10 - Sunderland MA

TABERLET P L GIELLY G PAUTOU amp J BOUVET (1991) Universal primers for amplificationof three non-coding regions of chloroplast DNA - Plant Mol Biol 17 1105-1109

TSUBOTA H Y AGENO B ESTEacuteBANEZ T YAMAGUCHI amp H DEGUCHI (2003)Molecular phylogeny of the Grimmiales (Musci) based on chloroplast rbcL sequences - Hikobia 1455-70

TSUBOTA H E DE LUNA D GONZAacuteLEZ MS IGNATOV amp H DEGUCHI (2004) Molecularphylogenetics and ordinal relationships based on analyses of a large-scale data set of 600 rbcLsequences of mosses - Hikobia 14 149-170

VITT DH (1984) Classification of the Bryopsida - In SCHUSTER RM (ed) New Manual ofBryology 2 696-759 Hattori Botanical Laboratory Nichinan Japan

VITT DH B GOFFINET amp T HEDDERSON (1998) 8 The ordinal classification of the mossesquestions and answers for the 1990s - In BATES JW NW ASHTON amp JG DUCKETT (eds)Bryology for the twenty-first century British Bryol Soc pp 113-123

Received 3 September 2007 accepted in revised form 30 October 2007

Page 2: botanica parcial 3

2

(hornworts) In contrast to the latter two groups mosses are scarcely characterisedin terms of morphological-anatomical synapomorphies At the molecular levelhowever all three bryophyte lineages are well circumscribed (eg Qiu et al 1998Stech et al 2003 Cox et al 2004 Shaw amp Renzaglia 2004 Groth-Malonek et al2005 Forrest et al 2006 Qiu et al 2006) A general overview of the present state ofbryophyte phylogeny was recently provided by Renzaglia et al (2007)

In the 19th and 20th century different and often contradictory classification systemsof mosses were published which either relied more on gametophytic or on sporophyticcharacters (summarised for example in Buck 2007) Nowadays the phylogeneticsignificance of morphological-anatomical characters can be evaluated based onmolecular phylogenies The most recent classifications of liverworts (Frey amp Stech2005 He-Nygreacuten et al 2006) hornworts (Stotler amp Crandall-Stotler 2005 Duff etal 2007) and mosses (Goffinet amp Buck 2004) already integrated molecular and non-molecular characters to provide a consensus of the current knowledge Howeverseveral suprageneric relationships within the mosses remained unresolved orambiguous at the time of the Goffinet amp Buck (2004) classification such as ordinalrelationships within the Bryidae and the closest relatives of pleurocarpous mossesA number of recent attempts shed more light on these problematic relationships(eg Tsubota et al 2004 Shaw et al 2005 Stech amp Quandt 2006 Bell et al 2007Goffinet et al 2007 contributions in Newton amp Tangney 2007 Quandt et al 2007this paper) Although some clades of the moss phylogeny are still partly contradictoryor do not receive significant statistical support these studies seem to converge on acommon hypothesis of moss relationship at suprageneric levels allowing us toestablish an updated and revised classification

In the present study a molecular phylogeny of the Bryopsida is presented based on anew approach ie the combined analysis of solely non-coding plastid markers (trnL

UAAintron atpB-rbcL spacer psbA-trnH spacer) The current state of moss systematicsis discussed with respect to the impact of this approach as well as recently publishedmolecular phylogenies and phylogenomic inferences Finally we propose a newsynopsis of the suprageneric classification of the Bryophyta which updates that ofGoffinet amp Buck (2004) A detailed description of the taxa down to genus level willbe provided by a forthcoming new edition of Englers Syllabus of Plant Familiesfor which additional taxonomic changes are made here

Material and methods

TAXON SAMPLING A molecular data set of 85 species of Bryopsida was assembled by compilingsequences from own previous analyses and by sequencing of herbarium material Voucher informationand GenBank accession numbers are summarised in Table 1 together with indications of the newlysequenced accessions From 21 species all three non-coding markers employed here were newlysequenced In few cases sequences available in GenBank were used to complete the data set Andreaearupestris Hedw (Andreaeopsida) and Pogonatum subulatum (Menzies ex Brid) Brid (Poly-trichopsida) were used as outgroup representatives

DNA EXTRACTION PCR AND SEQUENCING DNA was extracted using the mixer mill MM200 (Retsch)and following the method of Doyle amp Doyle (1990) PCR reactions for trnL intron and atpB-rbcLspacer followed the protocols given in Frey et al (1999) and Stech (2004) and were performed with

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primers CM

DM

(slightly modified after Taberlet et al 1991 see Frey et al 1999) and atpB-1rbcL-1(Chiang et al 1998) respectively For amplification of the psbA-trnH spacer primers psbAF(5-GTT ATG CAT GAA CGT AAT GCT C-3 Sang et al 1997) and trnHR-2 (5-CGC GCA TGGTGG ATT CAC AAT CC-3 slightly modified after Sang et al 1997) were used with a PCRprotocol of 5 min 94degC 35 cycles (30 sec 94degC 1 min 48degC 1 min 40 sec 72degC) 7 min 72degC PCRproducts were purified using DNA purification kits (Qiagen Macherey-Nagel) Sequencing wasperformed as described in Stech (2004) using the amplification primers

ALIGNMENT AND PHYLOGENETIC ANALYSES DNA sequences were manually aligned in PhyDE v0992(Muumlller et al 2005) Following Quandt et al (2003) and Quandt amp Stech (2005) inversions inputative hairpin secondary structures were positionally separated in the alignment their presence orabsence was not coded for the phylogenetic analyses Phylogenetic reconstructions under the maximumparsimony criterion were performed using winPAUP 40b10 (Swofford 2002) in combination withPRAP (Muumlller 2004) as implemented in SeqState (Muumlller 2005) PRAP generates command filesfor PAUP that allow parsimony ratchet searches as designed by Nixon (1999) Heuristic searchesunder parsimony were performed with the following options all characters equally weighted andunordered TBR branch swapping collapse branches if maximum branch length is zero MulTreesoption in effect gaps treated as missing data Initially a heuristic search with 1000 addition sequencereplicates was performed For the parsimony ratchet ten random addition cycles of 200 ratchetiterations each were used with TBR branch swapping on a randomly re-weighted data set (25 ofthe positions) Heuristic bootstrap searches were performed with 1000 replicates with 10 additionsequence replicates per bootstrap replicate

Results

In the present data set of non-coding plastid markers sequence lengths ranged from243 to 368 nucleotides (nt) in the trnL intron and from 445 to 615 nt in the atpB-rbcL spacer The psbA-trnH spacer was considerably shorter than the other twomarkers and ranged from 103 to 186 nt The combined alignment of sequences from85 ingroup and two outgroup taxa comprised 2430 positions (trnL intron 668 atpB-rbcL spacer 1366 psbA-trnH spacer 396 positions) The most variable regions withambiguous alignment (781 positions) were excluded from phylogenetic analysis Ofthe 1649 included positions 628 (381) were variable and 455 of the variablepositions (725 or 276 of the total number of positions) were parsimony-informative The trnL intron comprised 124 the atpB-rbcL spacer 286 and the psbA-trnH spacer 45 of these included parsimony-informative positions

The shortest trees found in the heuristic maximum parsimony analysis of the combineddata set had a length of 2433 steps By applying the parsimony ratchet 129 treeswere retained that were one step shorter (length 2432 CI = 0419 RI = 0624) Thestrict consensus tree of the ratchet analysis is shown in Fig 1 The ingroup (Bryopsida)is supported with 100 bootstrap support (BS) Diphysciidae are sister to theremaining Bryopsida with 54 BS Encalyptidae Funariidae Timmiidae andDicranidae all receive gt 95 BS while Bryidae are slightly less supported (89BS) Relationships between these major lineages are resolved but unsupported Atordinal level within the Bryidae a lower resolution is observed SplachnalesOrthotrichales Aulacomniales Hypnodendrales Hookeriales and Hypnales areresolved as monophyletic with 67-100 BS whereas Hedwigiales BartramialesBryales Orthodontiales and Rhizogoniales are not A closer relationship ofOrthotrichales with the pleurocarpous mosses sl than with the more basal ordersHedwigiales Bartramiales Splachnales and Bryales is indicated

7

Discussion

Classification of mosses - recent progress and the current state

For a long time mosses were subdivided into three main lineages the subclassesSphagnidae Andreaeidae and Bryidae (eg Fleischer 1920 Vitt 1984 Frahm ampFrey 1987) the latter with a number of (super-)orders (eg Frey 1977) Howevermolecular data confirmed that mosses comprise a number of isolated basal lineagesrepresented by morphologically and ecologically distinct extant taxa such as TakakiaSphagnum Andreaea Andreaeobryum Oedipodium Tetraphis the Polytrichaceaeand Buxbaumia which probably have long independent phylogenetic histories (cfNewton et al 2007) As a result of molecular phylogenies and a re-evaluation ofmorphological-anatomical characters the classification of mosses has changedconsiderably in the last few years with the main lineages nowadays treated atsubdivision class and subclass levels within division Bryophyta (eg Doweld 2001Ochyra et al 2003 Goffinet amp Buck 2004 this study)

Takakia and Sphagnum are the earliest diverging moss taxa in molecular phylogenies(eg Newton et al 2000 Beckert et al 2001 Cox et al 2004 Qiu et al 2006Newton et al 2007) That Takakia is a moss and not a liverwort was confirmed byanalysis of DNA sequences and phylogenomic characters such as the distribution ofmitochondrial introns (eg Beckert et al 2001) Its taxonomic status however stillremains to be clarified On the one hand most molecular studies resolve Takakiaand Sphagnum as sister genera although only partly with high statistical supportThese molecular topologies do not support the recognition of division Takakiophytaas proposed by Crandall-Stotler (1986) One the other hand no morphologicalsynapomorphies unite Takakia with Sphagnum and significant molecular differencesseparating Takakia from all other mosses were also observed For example a regionin the plastid ITS3 is similar to that of other land plants but absent in mosses(Samigullin et al 2002) and a transition in the trnL

UAA gene changing the anticodon

to CAA was otherwise only found in leptosporangiate ferns and Ginkgo (Quandt etal 2004) Thus ldquoresolution of Sphagnum - Takakia clade may be an artifactrdquo (Shawamp Renzaglia 2004) Also Goffinet amp Buck (2004) did not unite Takakia and Sphagnumunder a formal taxonomic rank but placed them into different informal superclassesIn our opinion Takakia should be treated at the same level as Sphagnophytina andBryophytina (cf Doweld 2001) ie as a subdivision of Bryophyta However morefundamental nomenclatural changes are necessary as the family name Takakiaceaewas not validated in the original publication by Hattori amp Inoue (1958) (article411 of ICBN McNeill et al 2006) and consequently all higher taxa erected laterare invalid The corrected taxonomic treatment of Takakia is provided here withsporophytic characters included in the latin diagnosis of Takakiaceae (see taxonomy)

Within Bryophytina we recognise four morphologically and molecularly isolatedbasal lineages as separated from the arthrodontous mosses (Bryopsida) Andreaeopsida(with linear capsule dehiscence) the operculate but eperistomate Oedipodiopsida aswell as Polytrichopsida and Tetraphidopsida with nematodontous peristomes A fifthclass Andreaeobryopsida was erected by Buck amp Goffinet (2000) but re-includedin Andreaeopsida as a subclass by Ochyra et al (2003) The systematic status of

8

Andreaeobryum macrosporum Steere amp BMMurray and possible relationships withAndreaea and Takakia were discussed by Murray (1988) and summarised includingmolecular results by Shaw amp Renzaglia (2004)

On the next lower level a number of morphologically and molecularly divergentlineages are nowadays treated as subclasses of Bryopsida Buxbaumiidae andDiphysciidae are generally branching off first in molecular topologies (eg Beckertet al 2001 Magombo 2003 Cox et al 2004) followed by Timmiidae Encalyptidaeand Funariidae as well as Dicranidae (haplolepideous mosses) sister to Bryidae slThese subclasses (except Buxbaumiidae not included) are also well recognizable inthe present analysis of non-coding plastid sequences (Fig 1)

The morphologically very different Encalyptidae and Funariidae are revealed assister groups although mostly without high support in several molecular phylogenies(eg Goffinet et al 2001 Cox et al 2004 Hedderson et al 2004 Tsubota et al2003 2004) and also in the present study (Fig 1) Goffinet et al (2007) confirmedthis relationship by phylogenomic evidence namely a large (71 kb) inversion in thechloroplast genome of Funariaceae Disceliaceae and Encalyptaceae but not inGigaspermaceae Consequently the latter family was separated at ordinal level fromthe two remaining families of Funariales by Goffinet et al (2007) GigaspermalesFunariales and Encalyptales may share a common ancestor according to some butnot all molecular phylogenies (eg Goffinet et al 2001 2007 Hedderson et al2004 but not in Tsubota et al 2004) Although ontogenetic data from peristomedevelopment may support their common ancestry (Goffinet et al 2007) unambiguousmorphological synapomorphies are lacking We therefore propose to treatGigaspermaceae at subclass level within the Bryopsida (see taxonomy)

The haplolepideous mosses (Dicranidae) are clearly supported as a monophyleticlineage which obviously evolved from a diplolepideous ancestor according to theirposition in the molecular trees (eg Newton et al 2000 Tsubota et al 2003 Cox etal 2004 Goffinet amp Buck 2004) Molecular studies suitable for inferring ordinaland family level relationships within Dicranidae either focused on the haplolepideousmosses (eg Stech 1999ab 2004 LaFarge et al 2000 2002 Tsubota et al 2003Hedderson et al 2004) or included more than 15 haplolepideous taxa in analyses ofa broader range of mosses (eg Goffinet et al 2001 Tsubota et al 2004 this study)Major lineages supported by these analyses are for example Grimmiales(Grimmiaceae Ptychomitriaceae and Seligeriaceae) Leucobryaceae (incl formerDicranaceae-Campylopoideae and Paraleucobryoideae pp) Dicranaceae sstr(Dicranoideae plus former Dicnemonaceae and Paraleucobryoideae pp) Pottiaceae(incl Cinclidotaceae and Splachnobryum) and Calymperaceae (probably exclOctoblepharum) Furthermore several genera and families belong to Dicranidaewhose systematic positions have been controversial (eg Stech et al 1999b LaFarge et al 2002 Hedderson et al 2004 OBrien 2007 Quandt et al 2007 thisstudy) Amphidium Archidium Catoscopium Drummondia EphemeraceaeErpodiaceae Mittenia (cf OBrien 2007 sequences in some earlier analyses werebased on misdentified specimens) Rhachitheciaceae Schistostega Splachnobryumand Wardia On the contrary several problems remain such as the circumscriptionof Ditrichaceae and relationships of the major haplolepideous lineages in general

9

Fig 1 Strict consensus tree of 129 most parsimonious trees inferred from combined trnLUAA

intronatpB-rbcL spacer and psbA-trnH spacer sequences of 85 taxa of Bryopsida as well as Andreaearupestris (Andreaeopsida) and Pogonatum subulatum (Polytrichopsida) as outgroup representativesBootstrap support values gt50 are depicted above the branches

10

Consequently resolving the phylogeny of Dicranidae with confidence is one of themajor future challenges in moss systematics

As mentioned above Dicranaceae are monophyletic in a narrow circumscriptionaccording to molecular data In contrast to former Campylopoideae andParaleucobryoideae the status of Rhabdoweisioideae (= Oncophoroideae Ochyra2002) and Dicranelloideae needs further consideration Stech (1999ab) suggestedto recognise RhabdoweisioideaeRhabdoweisiaceae in a broad sense includingDicranoweisia Amphidium and Aongstroemia Subsequent molecular analysesconfirmed a close relationship of the genera Arctoa Cynodontium DicranoweisiaKiaeria Oncophorus Oreoweisia Oreas Rhabdoweisia and Symblepharis althoughwithout significant support (La Farge et al 2002 Tsubota et al 2003 Hedderson etal 2004) With respect to the molecular evidence available so far we propose toelevate Oncophoroideae to family level to accomodate these genera and perhapsGlyphomitrium (cf Tsubota et al 2003) whereas we consider AongstroemiaDichodontium and Diobelonella to belong to Aongstroemiaceae (cf Stech 1999a)Amphidium is neither closely related to Dicranaceae sstr nor to Oncophoroideae(La Farge et al 2002 Tsubota et al 2003 Hedderson et al 2004 Stech 2004 thisstudy) and should be treated at family level rather than placed in Dicranaceae assubfam Amphidioideae (Ochyra et al 2003) The circumscription of Dicranelloideaeis more difficult to evaluate as few representatives have been included in molecularanalyses However Dicranella heteromalla (Hedw) Schimp as well as the generaCampylopodium and Microcampylopus are clearly separated from Dicranaceae sstr(Stech 1999a 2004 La Farge et al 2002 Tsubota et al 2003 Hedderson et al2004) and consequently the subfamily deserves family status as well Finallymolecular data showed that the genus Hypodontium does not belong to Pottiaceae(Hedderson et al 2004 Tsubota et al 2004) Taxonomic conclusions have not beendrawn from these results which is made up here (see taxonomy)

All mosses with diplolepideous-alternate peristomes together with Splachnales witha diplolepideous-opposite (Funaria-type) peristome form a monophyletic group inmolecular analyses (eg Newton et al 2000 Beckert et al 2001 Goffinet et al2001 Cox et al 2004 Tsubota et al 2004 references in Table 2) Differentclassifications of this by far most species-rich group of mosses were proposed (egVitt et al 1998 Ochyra et al 2003 Goffinet amp Buck 2004) However at least someof the recognised subclasses and superorders are paraphyletic according to themolecular topologies and assigning formal ranks to all evolutionarily significantmonophyletic entities is problematic if the main taxonomic framework of Bryophytaand Bryopsida should be maintained (cf discussion in Bell et al 2007) Thereforein the present synopsis only one subclass Bryidae is recognised for all diplolepideous-alternate mosses and Splachnales This broadly defined Bryidae is subdivided into13 orders most of them resolved as monophyletic in the majority of the phylogeneticanalyses summarised in Table 2 although with different levels of statistical supportin maximum parsimony analyses To define monophyletic lineages at supraordinallevel informal node-based names may be chosen according to Bell et al (2007) Forexample the pleurocarpous mosses (pleurocarpy sensu Bell amp Newton 2007) andtheir closest acrocarpous relatives (Orthodontiales to Hypnales) were already

11

Table 2 Taxon sampling and bootstrap support (BS) for Dicranidae Bryidae and orders within theBryidae in recent phylogenetic analyses (MP only) based on combined molecular markers Markersare given in square brackets (non-coding regions in bold) numbers of included taxa in brackets ++respective clade present with ge 80 BS + clade present with lt 80 BS - clade not present no oronly one representative included

Bell amp Newton OBrien Quandt et al Bell et al this study(2004) (2007) (2007) (2007)

[rbcL rps4 [atpB atpB- [rbcL rps4 [rbcL rps4 [atpB-rbcLnad5] rbcL rbcL trnL-F nad5] trnL-F nad5] psbA-trnH

rps4 trnL-F] trnL]

Dicranidae + (2) + (4) ++ (3) (1) ++ (19)Bryidae ++ (57) + (53) ++ (52) ++ (98) ++ (58)Hedwigiales ++ (2) (1) ++ (2) ++ (2) - (3)Bartramiales ++ (2) ++ (4) ++ (4) ++ (3) - (4)Splachnales (0) ++ (2) ++ (3) ++ (2) ++ (5)Bryales - (4) - (5) ++ (18) + (17) - (8)Orthotrichales (1) ++ (3) ++ (3) ++ (2) ++ (4)Orthodontiales + (4) + (4) + (3) + (6) - (3)Aulacomniales + (6) + (7) ++ (2) + (7) + (3)Rhizogoniales ++ (13) + (8) ++ (5) ++ (14) - (3)Hypnodendrales ++ (13) + (7) ++ (4) ++ (29) ++ (6)Ptychomniales ++ (3) ++ (3) (1) ++ (4) (1)Hookeriales - (4) + (2) (1) + (2) + (8)Hypnales - (5) - (7) ++ (5) ++ (10) + (10)

summarised under the informal node based name pleurcarpids (Bell et al 2007)and can be distinguished from a basal grade of acrocarpous or cladocarpous lineages(Hedwigiales to Orthotrichales) Within the latter monophyly of BartramialesSplachnales and Orthotrichales is well-supported in all analyses including two ormore taxa except Bartramiales in the present data set (cf Fig 1) In contrast Bryalesreceive significant support less frequently (but see Bell et al 2007 Quandt et al2007) Hedwigiales are well supported if only Hedwigia (Hedwigiaceae) andRhacocarpus (Rhacocarpaceae) are included whereas the monospecific Helicophyllum(Helicophyllaceae) is not closely related to these taxa but shows affinities withBartramiales (Goffinet et al 2001 this study) With respect to the differentmorphologies of Helicophyllaceae and Bartramiaceae however the former shouldbe separated at ordinal level (see taxonomy)

Clarifying relationships of the Orthotrichales is still a difficult issue Analyses ofsingle chloroplast markers or parsimony analyses of combined markers from differentgenomes mostly indicated a close relationship either with Splachnales (eg Cox etal 2000 Newton et al 2000 Tsubota et al 2004 Quandt et al 2007) or with thepleurocarpids (Goffinet et al 2001 this study) Although none of these alternativesis well-supported the latter seems more likely with regard to the moderately tomaximally supported Orthotrichales - pleurocarpid sister group relationship in allanalyses of mitochondrial data and in likelihood analyses of combined plastidmitochondrial markers (Beckert et al 2001 Quandt et al 2007)

12

The molecular polyphyly of Rhizogoniaceae (eg Bell amp Newton 2004) was solvedby the transfer of rhizogonioid genera into broadly defined Aulacomniaceae andOrthodontiaceae (Bell et al 2007) which now include both acrocarpous andpleurocarpous taxa These systematic changes are also comprehensible by non-molecular characters such as morphological traits shared by Mesochaete andAulacomnium heterostichum (Hedw) Bruch amp Schimp or the variously reducedperistomes of Orthodontiaceae pp in contrast to the generally fully developed Bryum-type peristomes of rhizogonioid and hypnodendroid mosses (Bell et al 2007) Theposition of the solely pleurocarpous Hypnodendrales sister to the former Hypnidaeled to the recognition of the informal group core pleurocarps (Bell et al 2007)The former Hypnidae (Ptychomniales Hookeriales and Hypnales summarised ashomocostate pleurocarps) are monophyletic in most molecular analyses (eg Goffinetet al 2001 Tsubota et al 2004 Bell et al 2007) with Ptychomniales being well-supported (Pedersen amp Newton 2007 Table 2) Clarifying relationships betweenHookeriales and Hypnales and within the latter is still a challenge but recent molecularstudies seem to support a sister group relationship of both orders (Bell et al 2007present study)

Phylogenetic utility of non-coding plastid markers

Non-coding plastid markers that comprise both variable and conserved regionssuch as the trnL

UAA intron have repeatedly been shown to possess potential for

resolving relationships at high taxonomic levels (eg Borsch et al 2003 Quandtet al 2004) Both the trnL intron and atpB-rbcL spacer were characterised indetail in mosses with respect to their structure and molecular evolution (Quandt ampStech 2005 Stech amp Quandt 2006) They include conservative regions that can beunambiguosly aligned and even parts of the more variable regions can be used ifrepeats hairpin loops etc are correctly identified and adequately treated in thephylogenetic analyses (eg Quandt et al 2003 Quandt amp Stech 2005) Using theatpB-rbcL spacer alone (Stech amp Quandt 2006) relationships of the major mosslineages were largely consistent with the ldquototal evidencerdquo molecular tree of Goffinetamp Buck (2004) However in addition to general limitations that result from singlemarker analyses the use of non-coding markers may pose further problems suchas a high amount of homoplasy resulting in low resolution or low statistical supportfor many clades Therefore several recent molecular studies of relationships withinBryidae have employed both coding and non-coding markers (Table 2)Nevertheless the usefulness of analyses of combined non-coding plastid markerscannot be ruled out In fact Fig 1 and Table 2 indicate a phylogenetic signal inthe present data set as many clades are recovered that are usually also resolvedin analyses of coding or combined coding and non-coding markers Especiallywith regard to statistical support however the present analysis is inferior tothose of other recent data sets especially Bell et al (2007) and Quandt et al(2007) In addition the non-coding markers used here are of different suitabilityand even the two intergenic spacers differ considerably from each other ThepsbA-trnH spacer contributes much less to the trees resolution than the atpB-rbcL spacer first because it is much shorter and second because relatively largeparts are attributed to hairpin loops or otherwise hypervariable regions These

13

results indicate that future studies should evaluate the molecular evolution andphylogenetic potential of new markers both coding and con-coding and choosethe most suitable ones in a combined analysis to resolve the remaining uncertaintiesin moss phylogeny

Taxonomy

Takakiaceae Stech amp WFrey stat nov

Plantae virides nusquam rhizophorae sine protonemate e caudicis rhizomatis erectae Caudicesrhizomati et axes geotropi radiformes frequenter intercalariter ramificantes sine phyllidiis cumpapillis mucilaginis rostratis Caules phyllidiiferi saepe furcati Phyllidia sine lamina et costadistincta profunde 2-4(-5)-lobata pluristratosa tristicha sed torsione spiraliter disposita Filumcentralium in ambabus generationibus (axibus gametophyti et setis) adest Plantae dioicae Antheridiaet archegonia nuda Sporophytum terminale solitarium Seta persistens Capsula tortilis admaturitatem schizocarpa secus unam rimam spiralem longitudinalem dehiscens Stomata etoperculum absunt peristomium nullum Calyptra mitriformis

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiaceae SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval (Art 411)

Takakiales Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiales SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval

Takakiales SHatt amp Inoue ex RMSchust J Hattori Bot Lab 26 224 1963 nom inval (cumdescr latin)

Takakiopsida Stech amp WFrey statnov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiopsida Goffinet amp WRBuck Monogr Syst Bot Missouri Bot Gard 98 232 2004 nominval

Takakiopsida Jia et al Acta Phytotax Sin 41 350 351 2003 nom nud

Takakiopsida Wang amp Wu Fl Bryophyt Sin 8 447 2004 nom inval (cum descr latin)

Takakiophytina Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue JHattori Bot Lab 19 137 1958

Gigaspermidae Stech amp WFrey subclass nov

Plantae acrocarpae terrestres stoloniferae ramis brevibus erectis Folia unicostata cellulis laxislaevibus Capsula plerumque valde rugosa gymnostomatica vel cleistocarpa stomata cum duabuscellulis sociis Ab Funariidis et Encalyptidis charactere phylogenomico (71-kb inversio abest)separatae

14

TYPUS Gigaspermum Lindb Oumlfversigt af Foumlrhandlingar Kongl Svenska Vetenskaps-Akademien21 599 1865

Amphidiaceae Stech stat nov

Based on Dicranaceae subfam Amphidioideae Ochyra in Ochyra Zarnowiec amp Bednarek-OchyraCens Cat Polish Mosses 110 2003

TYPUS Amphidium Schimp Coroll Bryol Eur 39 1856

Amphidiaceae AJESm Moss Fl Britain Ireland 2nd ed 657 2004 nom inval descr angl

Dicranellaceae Stech stat nov

Based on Dicranaceae subfam Dicranelloideae Lindb Utkast Eur Bladmoss 33 1878[lsquoUnderfamilje Dicranelleaersquo]

TYPUS Dicranella (MuumlllHal) Schimp Coroll Bryol Eur 13 1856

Oncophoraceae Stech stat nov

Based on Dicranaceae subfam Oncophoroideae Lindb Utkast Eur Bladmoss 34 1878[lsquoUnderfamilje Oncophoreaersquo]

TYPUS Oncophorus (Brid) Brid Bryol Univ 1 389 1826

Hypodontiaceae Stech fam nov

Plantae robustae characteribus morphologicis Pottiaceis et Calymperaceis similes sedcharacteribus molecularicis separatae Bracteae perichaetiales internae e basi vaginantes subulataevel aristatae Capsula aspectu succulenta cellulae exothecii incrassatae annulus magnopereabsens Peristomii dentes breves triangulati incurvati aurantiaci leves vel infirme verrucosiCalyptra cucullata

TYPUS Hypodontium MuumlllHal Hedwigia 38 96 1899

Helicophyllales Stech amp WFrey ord nov

Plantae acrocarpae prostratae tomentosae Folia dimorpha in duas series laterales et unam seriemventralem divisa Costa percurrens Cellulae hexagonae ad subquadratae papillosae Capsula immersacupulata ad oblonga infra orificium abrupte incurvata stomata destituta Peristomium nullum Sporaeisomorphae heteropolares granulatae

TYPUS Helicophyllum Brid Bryol Univ 2 771 1827

Synopsis of the suprageneric classification of BryophytaAuthor citations are in accordance with Art 492 of the Vienna Code (McNeill et al 2006)

Subdivision Takakiophytina Stech amp WFreyClass Takakiopsida Stech amp WFrey

Order Takakiales Stech amp WFreyTakakiaceae Stech amp WFrey

Subdivision Sphagnophytina DoweldClass Sphagnopsida Schimp

Order Sphagnales Limpr

15

Sphagnaceae DumortOrder Ambuchananiales Seppelt amp HACrum

Ambuchananiaceae Seppelt amp HACrumSubdivision Bryophytina Engler

Class Andreaeopsida JHSchaffnSubclass Andreaeidae Engl

Order Andreaeales LimprAndreaeaceae Dumort

Subclass Andreaeobryidae OchyraOrder Andreaeobryales BMMurray

Andreaeobryaceae Steere amp BMMurrayClass Oedipodiopsida Goffinet amp WRBuck

Order Oedipodiales Goffinet amp WRBuckOedipodiaceae Schimp

Class Tetraphidopsida Goffinet amp WRBuckOrder Tetraphidales MFleisch

Tetraphidaceae SchimpClass Polytrichopsida Doweld

Order Polytrichales MFleischPolytrichaceae Schwaumlgr

Class Bryopsida PaxSubclass Buxbaumiidae Doweld

Order Buxbaumiales MFleischBuxbaumiaceae Schimp

Subclass Diphysciidae OchyraOrder Diphysciales MFleisch

Diphysciaceae MFleischSubclass Timmiidae Ochyra

Order Timmiales OchyraTimmiaceae Schimp

Subclass Encalyptidae Ochyra Żarnowiec amp Bednarek-OchyraOrder Encalyptales Dixon

Encalyptaceae SchimpSubclass Funariidae Ochyra

Order Funariales MFleischFunariaceae Schwaumlgr Disceliaceae Schimp

Subclass Gigaspermidae Stech amp WFreyOrder Gigaspermales Goffinet Wickett OWerner Ros AJShaw amp CJCox

Gigaspermaceae LindbSubclass Dicranidae Doweld

Order Catoscopiales Ignatov amp IgnatovaCatoscopiaceae Broth

Order Scouleriales Goffinet amp WRBuckDrummondiaceae Goffinet Scouleriaceae SPChurchill

Order Bryoxiphiales HACrum amp LEAndersonBryoxiphiaceae Besch

16

Order Grimmiales MFleischGrimmiaceae Arn Ptychomitriaceae Schimp Seligeriaceae Schimp

Order Archidiales LimprArchidiaceae Schimp

Order Mitteniales ShawMitteniaceae Broth

Order Dicranales HPhilib ex MFleischAmphidiaceae Stech Aongstroemiaceae De Not BruchiaceaeSchimp Calymperaceae Kindb Dicranaceae Schimp Dicranel-laceae Stech Ditrichaceae Limpr Erpodiaceae Broth EustichiaceaeBroth Fissidentaceae Schimp Leucobryaceae Schimp Onco-phoraceae Stech Rhachitheciaceae HRob Schistostegaceae SchimpViridivelleraceae IGStone Wardiaceae Welch

Order Pottiales MFleischEphemeraceae Schimp Hypodontiaceae Stech PleurophascaceaeBroth Pottiaceae Schimp Serpotortellaceae WDReese amp RHZander

Subclass Bryidae EnglOrder Hedwigiales Ochyra

Hedwigiaceae Schimp Rhacocarpaceae KindbOrder Helicophyllales Stech amp WFrey

Helicophyllaceae BrothOrder Bartramiales DQuandt NEBell amp Stech

Bartramiaceae SchwaumlgrOrder Splachnales Ochyra

Meesiaceae Schimp Splachnaceae Grev amp ArnOrder Bryales Limpr

Bryaceae Schwaumlgr Leptostomataceae Schwaumlgr Mniaceae SchwaumlgrPhyllodrepaniaceae Crosby Pseudoditrichaceae Steere amp ZIwatsPulchrinodaceae DQuandt NEBell amp Stech

Order Orthotrichales DixonOrthotrichaceae Arn

Order Orthodontiales NEBell AENewton amp DQuandtOrthodontiaceae Goffinet

Order Aulacomniales NEBell AENewton amp DQuandtAulacomniaceae Schimp

Order Rhizogoniales Goffinet amp WRBuckRhizogoniaceae Broth

Order Hypnodendrales NEBell AENewton amp DQuandtBraithwaiteaceae NEBell AENewton amp DQuandt Hypnodendra-ceae Broth Pterobryellaceae WRBuck amp Vitt Racopilaceae Kindb

Order Ptychomniales WRBuck CJCox AJShaw amp GoffinetPtychomniaceae MFleisch

Order Hookeriales MFleischDaltoniaceae Schimp Hookeriaceae Schimp HypopterygiaceaeMitt Leucomiaceae Broth Pilotrichaceae Kindb SaulomataceaeWRBuck CJCox AJShaw amp Goffinet Schimperobryaceae WR

17

Buck CJCox AJShaw amp GoffinetOrder Hypnales WRBuck amp Vitt

Amblystegiaceae GRoth Anomodontaceae Kindb BrachytheciaceaeSchimp Calliergonaceae Vanderpoorten Hedenaumls CJCox amp AJShaw Catagoniaceae WRBuck amp Ireland Climaciaceae KindbCryphaeaceae Schimp Echinodiaceae Broth Entodontaceae KindbFabroniaceae Schimp Fontinalaceae Schimp Helodiaceae OchyraHeterocladiaceae Ignatov amp Ignatova Hylocomiaceae MFleischHypnaceae Schimp Lembophyllaceae Broth LeptodontaceaeSchimp Lepyrodontaceae Broth Leskeaceae Schimp Leucodon-taceae Schimp Meteoriaceae Kindb Microtheciellaceae HAMillamp AJHarr Myriniaceae Schimp Myuriaceae MFleisch NeckeraceaeSchimp Orthorrhynchiaceae SHLin Phyllogoniaceae KindbPlagiotheciaceae MFleisch Pleuroziopsidaceae Ireland Prionodon-taceae Broth Pseudoleskeaceae Schimp PseudoleskeellaceaeIgnatov amp Ignatova Pterigynandraceae Schimp PterobryaceaeKindb Pylaisiaceae Schimp Pylaisiadelphaceae Goffinet amp WRBuck Regmatodontaceae Broth Rhytidiaceae Broth RigodiaceaeHACrum Rutenbergiaceae MFleisch Scorpidiaceae Ignatov ampIgnatova Sematophyllaceae Broth Sorapillaceae MFleisch Ste-reophyllaceae WRBuck amp Ireland Symphyodontaceae MFleischTheliaceae MFleisch Thuidiaceae Schimp TrachylomataceaeWRBuck amp Vitt

Acknowledgements

Sincere thanks are due to JLReveal (Ithaca) as well as WFPrudhomme van Reine and JFVeldkamp(Leiden) for comments and discussions about suprafamilial taxonomy to DQuandt (Dresden) for providingDNA from Rhacocarpus and Bartramiaceae species and to BGiesicke (Berlin) for technical assistance

References

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BELL NE amp AE NEWTON (2004) Systematic studies of non-hypnanaean pleurocarps establishinga phylogenetic framework for investigating the origins of pleurocarpy - In GOFFINET BV HOLLOWELL amp R MAGILL (eds) Molecular systematics of bryophytes Monogr Syst BotMissouri Bot Gard 98 290-319

BELL NE amp AE NEWTON (2007) Pleurocarpy in the Rhizogoniaceous grade - In NEWTONAE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolution SystematicsAssociation Special Volume Series 71 41-64

BELL NE D QUANDT TJ OBRIEN amp AE NEWTON (2007) Taxonomy and phylogeny inthe earliest diverging pleurocarps square holes and bifurcating pegs - Bryologist 110 533-560

BORSCH T KW HILU D QUANDT V WILDE C NEINHUIS amp W BARTHLOTT(2003) Non-coding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms- J Evol Biol 16 558-576

18

BUCK WR (2007) The history of pleurocarp classification two steps forward one step back - InNEWTON AE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 1-18

BUCK WR amp B GOFFINET (2000) Morphology and classification of mosses - In SHAWAJ amp B GOFFINET (eds) Bryophyte Biology pp 71-123 Cambridge University PressCambridge

CHIANG TY BA SCHAAL amp CI PENG (1998) Universal primers for amplification andsequencing a noncoding spacer between atpB and rbcL genes of chloroplast DNA - Bot Bull AcadSin 39 245-250

COX CJ B GOFFINET AE NEWTON AJ SHAW amp TAJ HEDDERSON (2000)Phylogenetic relationships among the diplolepideous-alternate mosses (Bryidae) inferred from nuclearand chloroplast DNA sequences - Bryologist 103 224-241

COX CJ B GOFFINET AJ SHAW amp SB BOLES (2004) Phylogenetic relationships amongthe mosses based on heterogeneous Bayesian analysis of multiple genes from multiple genomiccompartments - Syst Bot 29 234-250

CRANDALL-STOTLER B (1986) Morphogenesis developmental anatomy and bryophytephylogenetics contra-indications of monophyly - J Bryol 14 1-23

CROSBY MR RE MAGILL B ALLEN amp S HE (1999) A checklist of the mosses - MissouriBotanical Garden St Louis Missouri

DOWELD A (2001) Prosyllabus Tracheophytorum - GEOS Moscow i-lxxx + 110 pp

DOYLE JJ amp JL DOYLE (1990) Isolation of plant DNA from fresh tissue - Focus 12 13-15

DUFF RJ JC VILLAREAL DC CARGILL amp KS RENZAGLIA (2007) Progress andchallenges towards developing a phylogeny and classification of the hornworts - Bryologist 110214-243

FLEISCHER M (1920) Natuumlrliches System der Laubmoose - Hedwigia 61 390-400

FORREST LL EC DAVIS DG LONG BJ CRANDALL-STOTLER A CLARK ampML HOLLINGSWORTH (2006) Unraveling the evolutionary history of the liverworts (Marchantio-phyta) multiple taxa genomes and analyses - Bryologist 109 303-334

FRAHM J-P amp W FREY (1987) Moosflora 2 Aufl - UTB 1250 Stuttgart

FREY W (1977) Neue Vorstellungen uumlber die Verwandtschaftsgruppen und die Stammesgeschichteder Laubmoose - In FREY W H HURKA amp F OBERWINKLER (Hrsg) Beitraumlge zur Biologieder Pflanzen pp 117-139 Stuttgart

FREY W amp M STECH (2005) A morpho-molecular classification of the liverworts (Hepa-ticophytina Bryophyta) - Nova Hedwigia 81 55-78

FREY W M STECH amp K MEIszligNER (1999) Chloroplast DNA-relationship in palaeoaustralLopidium concinnum (Hypopterygiaceae Musci) An example of steno-evolution in mosses Studiesin austral temperate rain forest bryophytes 2 - Plant Syst Evol 218 67-75

GOFFINET B amp WR BUCK (2004) Systematics of Bryophyta (mosses) from molecules to arevised classification - In GOFFINET B V HOLLOWELL amp R MAGILL (eds) Molecularsystematics of bryophytes Monogr Syst Bot Missouri Bot Gard 98 205-239

GOFFINET B CJ COX AJ SHAW amp TAJ HEDDERSON (2001) The Bryophyta (mosses)Systematic and evolutionary inferences from an rps4 gene (cpDNA) phylogeny - Ann Bot 87191-208

GOFFINET B NJ WICKETT O WERNER RM ROS AJ SHAW amp CJ COX (2007)Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae(Bryophyta) - Ann Bot 99 747-753

19

GROTH-MALONEK M D PRUCHNER F GREWE amp V KNOOP (2005) Ancestors oftrans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosseswith vascular plants - Mol Biol Evol 22 117-125

HATTORI S amp H INOUE (1958) Preliminary report on Takakia lepidozioides - J Hattori BotLab 19 133-137

HE-NYGREacuteN X A JUSLEacuteN I AHONEN D GLENNY amp S PIIPPO (2006) Illuminating theevolutionary history of liverworts (Marchantiophyta) - towards a natural classification - Cladistics22 1-31

HEDDERSON TAJ DJ MURRAY CJ COX amp TL NOWELL (2004) Phylogeneticrelationships of haplolepideous mosses (Dicranidae) inferred from rps4 gene sequences - Syst Bot29 29-41

LA FARGE C BD MISHER JA WHEELER DP WALL K JOHANNES S SCHAFFERamp AJ SHAW (2000) Phylogenetic relationships within the haplolepideous mosses - Bryologist103 257-276

LA FARGE C AJ SHAW amp DH VITT (2002) The circumscription of the Dicranaceae(Bryopsida) based on the chloroplast regions trnL-trnF and rps4 - Syst Bot 27 435-452

MAGOMBO ZLK (2003) The phylogeny of basal peristomate mosses evidence from cpDNAand implications for peristome evolution - Syst Bot 28 24-38

MCNEILL J FR BARRIE HM BURDET V DEMOULIN DL HAWKSWORTHK MARHOLD DH NICOLSON J PRADO PC SILVA JE SKOG JH WIERSEMA ampNJ TURLAND (2006) International Code of Botanical Nomenclature (Vienna Code) - RegnumVegetabile 146 1-568

MUumlLLER K (2004) PRAP - computation of Bremer support for large data sets - Mol PhylogenetEvol 31 780-782

MUumlLLER K (2005) SeqState - primer design and sequence statistics for phylogenetic DNA datasets - Appl Bioinformatics 4 65-69

MUumlLLER K D QUANDT J MUumlLLER amp C NEINHUIS (2005) PhyDE v0992 PhylogeneticData Editor - httpwwwphydede

MURRAY BM (1988) Systematics of the Andreaeopsida (Bryophyta) two orders with links toTakakia - Nova Hedwigia Beih 90 289-336

NEWTON AE amp RS TANGNEY (eds) (2007) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 CRC Press Boca Raton 434 pp

NEWTON AE CJ COX JG DUCKETT JA WHEELER B GOFFINET TAJ HEDDER-SON amp BD MISHLER (2000) Evolution of the major moss lineages Phylogenetic analyses basedon multiple gene sequences and morphology - Bryologist 103 187-211

NEWTON AE N WIKSTROumlM NE BELL LL FORREST amp MS IGNATOV (2007)Dating the diversification of the pleurocarpous mosses - In NEWTON AE amp RS TANGNEY(eds) Pleurocarpous mosses systematics and evolution Systematics Association Special VolumeSeries 71 337-366

NIXON KC (1999) The parsimony ratchet a new method for rapid parsimony analysis - Cladistics15 407-411

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OCHYRA R (2002) Nomenclatural changes in subfamilies of the Dicranaceae - CryptogamieBryol 23 345-349

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Received 3 September 2007 accepted in revised form 30 October 2007

Page 3: botanica parcial 3

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4135

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Y31

2894

Hym

enod

onto

psis

mni

oide

s (H

ook

)F

rey

amp S

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man

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EU

1865

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U18

6625

EU

1635

60N

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ell

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ton

amp D

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ndt

01

-186

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01-0

9

Tab

le 1

con

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ed

5

Rhi

zogo

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20-

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6560

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1866

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1865

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6622

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1635

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) B

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-11

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6562

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1866

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3558

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EU

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1635

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Pfe

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210

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R

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6565

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1866

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3562

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EU

1865

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U18

6628

EU

1635

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1865

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U18

6626

EU

1635

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Ptyc

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chom

nion

pty

choc

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n (S

chw

aumlgr

)F

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amp S

chau

man

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F

rey

EU

1865

70E

U18

6632

EU

1635

67M

itt

01

-266

aH

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riac

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Hoo

keri

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cens

(H

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m

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8804

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F15

2380

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1866

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U16

3570

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tech

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U18

6571

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1866

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U16

3568

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04-1

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1865

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U18

6634

EU

1635

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1866

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3573

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Fre

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Sch

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ann

F

Fre

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U18

6575

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1866

40E

U16

3578

01-1

87a

Tab

le 1

con

tinu

ed

6

primers CM

DM

(slightly modified after Taberlet et al 1991 see Frey et al 1999) and atpB-1rbcL-1(Chiang et al 1998) respectively For amplification of the psbA-trnH spacer primers psbAF(5-GTT ATG CAT GAA CGT AAT GCT C-3 Sang et al 1997) and trnHR-2 (5-CGC GCA TGGTGG ATT CAC AAT CC-3 slightly modified after Sang et al 1997) were used with a PCRprotocol of 5 min 94degC 35 cycles (30 sec 94degC 1 min 48degC 1 min 40 sec 72degC) 7 min 72degC PCRproducts were purified using DNA purification kits (Qiagen Macherey-Nagel) Sequencing wasperformed as described in Stech (2004) using the amplification primers

ALIGNMENT AND PHYLOGENETIC ANALYSES DNA sequences were manually aligned in PhyDE v0992(Muumlller et al 2005) Following Quandt et al (2003) and Quandt amp Stech (2005) inversions inputative hairpin secondary structures were positionally separated in the alignment their presence orabsence was not coded for the phylogenetic analyses Phylogenetic reconstructions under the maximumparsimony criterion were performed using winPAUP 40b10 (Swofford 2002) in combination withPRAP (Muumlller 2004) as implemented in SeqState (Muumlller 2005) PRAP generates command filesfor PAUP that allow parsimony ratchet searches as designed by Nixon (1999) Heuristic searchesunder parsimony were performed with the following options all characters equally weighted andunordered TBR branch swapping collapse branches if maximum branch length is zero MulTreesoption in effect gaps treated as missing data Initially a heuristic search with 1000 addition sequencereplicates was performed For the parsimony ratchet ten random addition cycles of 200 ratchetiterations each were used with TBR branch swapping on a randomly re-weighted data set (25 ofthe positions) Heuristic bootstrap searches were performed with 1000 replicates with 10 additionsequence replicates per bootstrap replicate

Results

In the present data set of non-coding plastid markers sequence lengths ranged from243 to 368 nucleotides (nt) in the trnL intron and from 445 to 615 nt in the atpB-rbcL spacer The psbA-trnH spacer was considerably shorter than the other twomarkers and ranged from 103 to 186 nt The combined alignment of sequences from85 ingroup and two outgroup taxa comprised 2430 positions (trnL intron 668 atpB-rbcL spacer 1366 psbA-trnH spacer 396 positions) The most variable regions withambiguous alignment (781 positions) were excluded from phylogenetic analysis Ofthe 1649 included positions 628 (381) were variable and 455 of the variablepositions (725 or 276 of the total number of positions) were parsimony-informative The trnL intron comprised 124 the atpB-rbcL spacer 286 and the psbA-trnH spacer 45 of these included parsimony-informative positions

The shortest trees found in the heuristic maximum parsimony analysis of the combineddata set had a length of 2433 steps By applying the parsimony ratchet 129 treeswere retained that were one step shorter (length 2432 CI = 0419 RI = 0624) Thestrict consensus tree of the ratchet analysis is shown in Fig 1 The ingroup (Bryopsida)is supported with 100 bootstrap support (BS) Diphysciidae are sister to theremaining Bryopsida with 54 BS Encalyptidae Funariidae Timmiidae andDicranidae all receive gt 95 BS while Bryidae are slightly less supported (89BS) Relationships between these major lineages are resolved but unsupported Atordinal level within the Bryidae a lower resolution is observed SplachnalesOrthotrichales Aulacomniales Hypnodendrales Hookeriales and Hypnales areresolved as monophyletic with 67-100 BS whereas Hedwigiales BartramialesBryales Orthodontiales and Rhizogoniales are not A closer relationship ofOrthotrichales with the pleurocarpous mosses sl than with the more basal ordersHedwigiales Bartramiales Splachnales and Bryales is indicated

7

Discussion

Classification of mosses - recent progress and the current state

For a long time mosses were subdivided into three main lineages the subclassesSphagnidae Andreaeidae and Bryidae (eg Fleischer 1920 Vitt 1984 Frahm ampFrey 1987) the latter with a number of (super-)orders (eg Frey 1977) Howevermolecular data confirmed that mosses comprise a number of isolated basal lineagesrepresented by morphologically and ecologically distinct extant taxa such as TakakiaSphagnum Andreaea Andreaeobryum Oedipodium Tetraphis the Polytrichaceaeand Buxbaumia which probably have long independent phylogenetic histories (cfNewton et al 2007) As a result of molecular phylogenies and a re-evaluation ofmorphological-anatomical characters the classification of mosses has changedconsiderably in the last few years with the main lineages nowadays treated atsubdivision class and subclass levels within division Bryophyta (eg Doweld 2001Ochyra et al 2003 Goffinet amp Buck 2004 this study)

Takakia and Sphagnum are the earliest diverging moss taxa in molecular phylogenies(eg Newton et al 2000 Beckert et al 2001 Cox et al 2004 Qiu et al 2006Newton et al 2007) That Takakia is a moss and not a liverwort was confirmed byanalysis of DNA sequences and phylogenomic characters such as the distribution ofmitochondrial introns (eg Beckert et al 2001) Its taxonomic status however stillremains to be clarified On the one hand most molecular studies resolve Takakiaand Sphagnum as sister genera although only partly with high statistical supportThese molecular topologies do not support the recognition of division Takakiophytaas proposed by Crandall-Stotler (1986) One the other hand no morphologicalsynapomorphies unite Takakia with Sphagnum and significant molecular differencesseparating Takakia from all other mosses were also observed For example a regionin the plastid ITS3 is similar to that of other land plants but absent in mosses(Samigullin et al 2002) and a transition in the trnL

UAA gene changing the anticodon

to CAA was otherwise only found in leptosporangiate ferns and Ginkgo (Quandt etal 2004) Thus ldquoresolution of Sphagnum - Takakia clade may be an artifactrdquo (Shawamp Renzaglia 2004) Also Goffinet amp Buck (2004) did not unite Takakia and Sphagnumunder a formal taxonomic rank but placed them into different informal superclassesIn our opinion Takakia should be treated at the same level as Sphagnophytina andBryophytina (cf Doweld 2001) ie as a subdivision of Bryophyta However morefundamental nomenclatural changes are necessary as the family name Takakiaceaewas not validated in the original publication by Hattori amp Inoue (1958) (article411 of ICBN McNeill et al 2006) and consequently all higher taxa erected laterare invalid The corrected taxonomic treatment of Takakia is provided here withsporophytic characters included in the latin diagnosis of Takakiaceae (see taxonomy)

Within Bryophytina we recognise four morphologically and molecularly isolatedbasal lineages as separated from the arthrodontous mosses (Bryopsida) Andreaeopsida(with linear capsule dehiscence) the operculate but eperistomate Oedipodiopsida aswell as Polytrichopsida and Tetraphidopsida with nematodontous peristomes A fifthclass Andreaeobryopsida was erected by Buck amp Goffinet (2000) but re-includedin Andreaeopsida as a subclass by Ochyra et al (2003) The systematic status of

8

Andreaeobryum macrosporum Steere amp BMMurray and possible relationships withAndreaea and Takakia were discussed by Murray (1988) and summarised includingmolecular results by Shaw amp Renzaglia (2004)

On the next lower level a number of morphologically and molecularly divergentlineages are nowadays treated as subclasses of Bryopsida Buxbaumiidae andDiphysciidae are generally branching off first in molecular topologies (eg Beckertet al 2001 Magombo 2003 Cox et al 2004) followed by Timmiidae Encalyptidaeand Funariidae as well as Dicranidae (haplolepideous mosses) sister to Bryidae slThese subclasses (except Buxbaumiidae not included) are also well recognizable inthe present analysis of non-coding plastid sequences (Fig 1)

The morphologically very different Encalyptidae and Funariidae are revealed assister groups although mostly without high support in several molecular phylogenies(eg Goffinet et al 2001 Cox et al 2004 Hedderson et al 2004 Tsubota et al2003 2004) and also in the present study (Fig 1) Goffinet et al (2007) confirmedthis relationship by phylogenomic evidence namely a large (71 kb) inversion in thechloroplast genome of Funariaceae Disceliaceae and Encalyptaceae but not inGigaspermaceae Consequently the latter family was separated at ordinal level fromthe two remaining families of Funariales by Goffinet et al (2007) GigaspermalesFunariales and Encalyptales may share a common ancestor according to some butnot all molecular phylogenies (eg Goffinet et al 2001 2007 Hedderson et al2004 but not in Tsubota et al 2004) Although ontogenetic data from peristomedevelopment may support their common ancestry (Goffinet et al 2007) unambiguousmorphological synapomorphies are lacking We therefore propose to treatGigaspermaceae at subclass level within the Bryopsida (see taxonomy)

The haplolepideous mosses (Dicranidae) are clearly supported as a monophyleticlineage which obviously evolved from a diplolepideous ancestor according to theirposition in the molecular trees (eg Newton et al 2000 Tsubota et al 2003 Cox etal 2004 Goffinet amp Buck 2004) Molecular studies suitable for inferring ordinaland family level relationships within Dicranidae either focused on the haplolepideousmosses (eg Stech 1999ab 2004 LaFarge et al 2000 2002 Tsubota et al 2003Hedderson et al 2004) or included more than 15 haplolepideous taxa in analyses ofa broader range of mosses (eg Goffinet et al 2001 Tsubota et al 2004 this study)Major lineages supported by these analyses are for example Grimmiales(Grimmiaceae Ptychomitriaceae and Seligeriaceae) Leucobryaceae (incl formerDicranaceae-Campylopoideae and Paraleucobryoideae pp) Dicranaceae sstr(Dicranoideae plus former Dicnemonaceae and Paraleucobryoideae pp) Pottiaceae(incl Cinclidotaceae and Splachnobryum) and Calymperaceae (probably exclOctoblepharum) Furthermore several genera and families belong to Dicranidaewhose systematic positions have been controversial (eg Stech et al 1999b LaFarge et al 2002 Hedderson et al 2004 OBrien 2007 Quandt et al 2007 thisstudy) Amphidium Archidium Catoscopium Drummondia EphemeraceaeErpodiaceae Mittenia (cf OBrien 2007 sequences in some earlier analyses werebased on misdentified specimens) Rhachitheciaceae Schistostega Splachnobryumand Wardia On the contrary several problems remain such as the circumscriptionof Ditrichaceae and relationships of the major haplolepideous lineages in general

9

Fig 1 Strict consensus tree of 129 most parsimonious trees inferred from combined trnLUAA

intronatpB-rbcL spacer and psbA-trnH spacer sequences of 85 taxa of Bryopsida as well as Andreaearupestris (Andreaeopsida) and Pogonatum subulatum (Polytrichopsida) as outgroup representativesBootstrap support values gt50 are depicted above the branches

10

Consequently resolving the phylogeny of Dicranidae with confidence is one of themajor future challenges in moss systematics

As mentioned above Dicranaceae are monophyletic in a narrow circumscriptionaccording to molecular data In contrast to former Campylopoideae andParaleucobryoideae the status of Rhabdoweisioideae (= Oncophoroideae Ochyra2002) and Dicranelloideae needs further consideration Stech (1999ab) suggestedto recognise RhabdoweisioideaeRhabdoweisiaceae in a broad sense includingDicranoweisia Amphidium and Aongstroemia Subsequent molecular analysesconfirmed a close relationship of the genera Arctoa Cynodontium DicranoweisiaKiaeria Oncophorus Oreoweisia Oreas Rhabdoweisia and Symblepharis althoughwithout significant support (La Farge et al 2002 Tsubota et al 2003 Hedderson etal 2004) With respect to the molecular evidence available so far we propose toelevate Oncophoroideae to family level to accomodate these genera and perhapsGlyphomitrium (cf Tsubota et al 2003) whereas we consider AongstroemiaDichodontium and Diobelonella to belong to Aongstroemiaceae (cf Stech 1999a)Amphidium is neither closely related to Dicranaceae sstr nor to Oncophoroideae(La Farge et al 2002 Tsubota et al 2003 Hedderson et al 2004 Stech 2004 thisstudy) and should be treated at family level rather than placed in Dicranaceae assubfam Amphidioideae (Ochyra et al 2003) The circumscription of Dicranelloideaeis more difficult to evaluate as few representatives have been included in molecularanalyses However Dicranella heteromalla (Hedw) Schimp as well as the generaCampylopodium and Microcampylopus are clearly separated from Dicranaceae sstr(Stech 1999a 2004 La Farge et al 2002 Tsubota et al 2003 Hedderson et al2004) and consequently the subfamily deserves family status as well Finallymolecular data showed that the genus Hypodontium does not belong to Pottiaceae(Hedderson et al 2004 Tsubota et al 2004) Taxonomic conclusions have not beendrawn from these results which is made up here (see taxonomy)

All mosses with diplolepideous-alternate peristomes together with Splachnales witha diplolepideous-opposite (Funaria-type) peristome form a monophyletic group inmolecular analyses (eg Newton et al 2000 Beckert et al 2001 Goffinet et al2001 Cox et al 2004 Tsubota et al 2004 references in Table 2) Differentclassifications of this by far most species-rich group of mosses were proposed (egVitt et al 1998 Ochyra et al 2003 Goffinet amp Buck 2004) However at least someof the recognised subclasses and superorders are paraphyletic according to themolecular topologies and assigning formal ranks to all evolutionarily significantmonophyletic entities is problematic if the main taxonomic framework of Bryophytaand Bryopsida should be maintained (cf discussion in Bell et al 2007) Thereforein the present synopsis only one subclass Bryidae is recognised for all diplolepideous-alternate mosses and Splachnales This broadly defined Bryidae is subdivided into13 orders most of them resolved as monophyletic in the majority of the phylogeneticanalyses summarised in Table 2 although with different levels of statistical supportin maximum parsimony analyses To define monophyletic lineages at supraordinallevel informal node-based names may be chosen according to Bell et al (2007) Forexample the pleurocarpous mosses (pleurocarpy sensu Bell amp Newton 2007) andtheir closest acrocarpous relatives (Orthodontiales to Hypnales) were already

11

Table 2 Taxon sampling and bootstrap support (BS) for Dicranidae Bryidae and orders within theBryidae in recent phylogenetic analyses (MP only) based on combined molecular markers Markersare given in square brackets (non-coding regions in bold) numbers of included taxa in brackets ++respective clade present with ge 80 BS + clade present with lt 80 BS - clade not present no oronly one representative included

Bell amp Newton OBrien Quandt et al Bell et al this study(2004) (2007) (2007) (2007)

[rbcL rps4 [atpB atpB- [rbcL rps4 [rbcL rps4 [atpB-rbcLnad5] rbcL rbcL trnL-F nad5] trnL-F nad5] psbA-trnH

rps4 trnL-F] trnL]

Dicranidae + (2) + (4) ++ (3) (1) ++ (19)Bryidae ++ (57) + (53) ++ (52) ++ (98) ++ (58)Hedwigiales ++ (2) (1) ++ (2) ++ (2) - (3)Bartramiales ++ (2) ++ (4) ++ (4) ++ (3) - (4)Splachnales (0) ++ (2) ++ (3) ++ (2) ++ (5)Bryales - (4) - (5) ++ (18) + (17) - (8)Orthotrichales (1) ++ (3) ++ (3) ++ (2) ++ (4)Orthodontiales + (4) + (4) + (3) + (6) - (3)Aulacomniales + (6) + (7) ++ (2) + (7) + (3)Rhizogoniales ++ (13) + (8) ++ (5) ++ (14) - (3)Hypnodendrales ++ (13) + (7) ++ (4) ++ (29) ++ (6)Ptychomniales ++ (3) ++ (3) (1) ++ (4) (1)Hookeriales - (4) + (2) (1) + (2) + (8)Hypnales - (5) - (7) ++ (5) ++ (10) + (10)

summarised under the informal node based name pleurcarpids (Bell et al 2007)and can be distinguished from a basal grade of acrocarpous or cladocarpous lineages(Hedwigiales to Orthotrichales) Within the latter monophyly of BartramialesSplachnales and Orthotrichales is well-supported in all analyses including two ormore taxa except Bartramiales in the present data set (cf Fig 1) In contrast Bryalesreceive significant support less frequently (but see Bell et al 2007 Quandt et al2007) Hedwigiales are well supported if only Hedwigia (Hedwigiaceae) andRhacocarpus (Rhacocarpaceae) are included whereas the monospecific Helicophyllum(Helicophyllaceae) is not closely related to these taxa but shows affinities withBartramiales (Goffinet et al 2001 this study) With respect to the differentmorphologies of Helicophyllaceae and Bartramiaceae however the former shouldbe separated at ordinal level (see taxonomy)

Clarifying relationships of the Orthotrichales is still a difficult issue Analyses ofsingle chloroplast markers or parsimony analyses of combined markers from differentgenomes mostly indicated a close relationship either with Splachnales (eg Cox etal 2000 Newton et al 2000 Tsubota et al 2004 Quandt et al 2007) or with thepleurocarpids (Goffinet et al 2001 this study) Although none of these alternativesis well-supported the latter seems more likely with regard to the moderately tomaximally supported Orthotrichales - pleurocarpid sister group relationship in allanalyses of mitochondrial data and in likelihood analyses of combined plastidmitochondrial markers (Beckert et al 2001 Quandt et al 2007)

12

The molecular polyphyly of Rhizogoniaceae (eg Bell amp Newton 2004) was solvedby the transfer of rhizogonioid genera into broadly defined Aulacomniaceae andOrthodontiaceae (Bell et al 2007) which now include both acrocarpous andpleurocarpous taxa These systematic changes are also comprehensible by non-molecular characters such as morphological traits shared by Mesochaete andAulacomnium heterostichum (Hedw) Bruch amp Schimp or the variously reducedperistomes of Orthodontiaceae pp in contrast to the generally fully developed Bryum-type peristomes of rhizogonioid and hypnodendroid mosses (Bell et al 2007) Theposition of the solely pleurocarpous Hypnodendrales sister to the former Hypnidaeled to the recognition of the informal group core pleurocarps (Bell et al 2007)The former Hypnidae (Ptychomniales Hookeriales and Hypnales summarised ashomocostate pleurocarps) are monophyletic in most molecular analyses (eg Goffinetet al 2001 Tsubota et al 2004 Bell et al 2007) with Ptychomniales being well-supported (Pedersen amp Newton 2007 Table 2) Clarifying relationships betweenHookeriales and Hypnales and within the latter is still a challenge but recent molecularstudies seem to support a sister group relationship of both orders (Bell et al 2007present study)

Phylogenetic utility of non-coding plastid markers

Non-coding plastid markers that comprise both variable and conserved regionssuch as the trnL

UAA intron have repeatedly been shown to possess potential for

resolving relationships at high taxonomic levels (eg Borsch et al 2003 Quandtet al 2004) Both the trnL intron and atpB-rbcL spacer were characterised indetail in mosses with respect to their structure and molecular evolution (Quandt ampStech 2005 Stech amp Quandt 2006) They include conservative regions that can beunambiguosly aligned and even parts of the more variable regions can be used ifrepeats hairpin loops etc are correctly identified and adequately treated in thephylogenetic analyses (eg Quandt et al 2003 Quandt amp Stech 2005) Using theatpB-rbcL spacer alone (Stech amp Quandt 2006) relationships of the major mosslineages were largely consistent with the ldquototal evidencerdquo molecular tree of Goffinetamp Buck (2004) However in addition to general limitations that result from singlemarker analyses the use of non-coding markers may pose further problems suchas a high amount of homoplasy resulting in low resolution or low statistical supportfor many clades Therefore several recent molecular studies of relationships withinBryidae have employed both coding and non-coding markers (Table 2)Nevertheless the usefulness of analyses of combined non-coding plastid markerscannot be ruled out In fact Fig 1 and Table 2 indicate a phylogenetic signal inthe present data set as many clades are recovered that are usually also resolvedin analyses of coding or combined coding and non-coding markers Especiallywith regard to statistical support however the present analysis is inferior tothose of other recent data sets especially Bell et al (2007) and Quandt et al(2007) In addition the non-coding markers used here are of different suitabilityand even the two intergenic spacers differ considerably from each other ThepsbA-trnH spacer contributes much less to the trees resolution than the atpB-rbcL spacer first because it is much shorter and second because relatively largeparts are attributed to hairpin loops or otherwise hypervariable regions These

13

results indicate that future studies should evaluate the molecular evolution andphylogenetic potential of new markers both coding and con-coding and choosethe most suitable ones in a combined analysis to resolve the remaining uncertaintiesin moss phylogeny

Taxonomy

Takakiaceae Stech amp WFrey stat nov

Plantae virides nusquam rhizophorae sine protonemate e caudicis rhizomatis erectae Caudicesrhizomati et axes geotropi radiformes frequenter intercalariter ramificantes sine phyllidiis cumpapillis mucilaginis rostratis Caules phyllidiiferi saepe furcati Phyllidia sine lamina et costadistincta profunde 2-4(-5)-lobata pluristratosa tristicha sed torsione spiraliter disposita Filumcentralium in ambabus generationibus (axibus gametophyti et setis) adest Plantae dioicae Antheridiaet archegonia nuda Sporophytum terminale solitarium Seta persistens Capsula tortilis admaturitatem schizocarpa secus unam rimam spiralem longitudinalem dehiscens Stomata etoperculum absunt peristomium nullum Calyptra mitriformis

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiaceae SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval (Art 411)

Takakiales Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiales SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval

Takakiales SHatt amp Inoue ex RMSchust J Hattori Bot Lab 26 224 1963 nom inval (cumdescr latin)

Takakiopsida Stech amp WFrey statnov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiopsida Goffinet amp WRBuck Monogr Syst Bot Missouri Bot Gard 98 232 2004 nominval

Takakiopsida Jia et al Acta Phytotax Sin 41 350 351 2003 nom nud

Takakiopsida Wang amp Wu Fl Bryophyt Sin 8 447 2004 nom inval (cum descr latin)

Takakiophytina Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue JHattori Bot Lab 19 137 1958

Gigaspermidae Stech amp WFrey subclass nov

Plantae acrocarpae terrestres stoloniferae ramis brevibus erectis Folia unicostata cellulis laxislaevibus Capsula plerumque valde rugosa gymnostomatica vel cleistocarpa stomata cum duabuscellulis sociis Ab Funariidis et Encalyptidis charactere phylogenomico (71-kb inversio abest)separatae

14

TYPUS Gigaspermum Lindb Oumlfversigt af Foumlrhandlingar Kongl Svenska Vetenskaps-Akademien21 599 1865

Amphidiaceae Stech stat nov

Based on Dicranaceae subfam Amphidioideae Ochyra in Ochyra Zarnowiec amp Bednarek-OchyraCens Cat Polish Mosses 110 2003

TYPUS Amphidium Schimp Coroll Bryol Eur 39 1856

Amphidiaceae AJESm Moss Fl Britain Ireland 2nd ed 657 2004 nom inval descr angl

Dicranellaceae Stech stat nov

Based on Dicranaceae subfam Dicranelloideae Lindb Utkast Eur Bladmoss 33 1878[lsquoUnderfamilje Dicranelleaersquo]

TYPUS Dicranella (MuumlllHal) Schimp Coroll Bryol Eur 13 1856

Oncophoraceae Stech stat nov

Based on Dicranaceae subfam Oncophoroideae Lindb Utkast Eur Bladmoss 34 1878[lsquoUnderfamilje Oncophoreaersquo]

TYPUS Oncophorus (Brid) Brid Bryol Univ 1 389 1826

Hypodontiaceae Stech fam nov

Plantae robustae characteribus morphologicis Pottiaceis et Calymperaceis similes sedcharacteribus molecularicis separatae Bracteae perichaetiales internae e basi vaginantes subulataevel aristatae Capsula aspectu succulenta cellulae exothecii incrassatae annulus magnopereabsens Peristomii dentes breves triangulati incurvati aurantiaci leves vel infirme verrucosiCalyptra cucullata

TYPUS Hypodontium MuumlllHal Hedwigia 38 96 1899

Helicophyllales Stech amp WFrey ord nov

Plantae acrocarpae prostratae tomentosae Folia dimorpha in duas series laterales et unam seriemventralem divisa Costa percurrens Cellulae hexagonae ad subquadratae papillosae Capsula immersacupulata ad oblonga infra orificium abrupte incurvata stomata destituta Peristomium nullum Sporaeisomorphae heteropolares granulatae

TYPUS Helicophyllum Brid Bryol Univ 2 771 1827

Synopsis of the suprageneric classification of BryophytaAuthor citations are in accordance with Art 492 of the Vienna Code (McNeill et al 2006)

Subdivision Takakiophytina Stech amp WFreyClass Takakiopsida Stech amp WFrey

Order Takakiales Stech amp WFreyTakakiaceae Stech amp WFrey

Subdivision Sphagnophytina DoweldClass Sphagnopsida Schimp

Order Sphagnales Limpr

15

Sphagnaceae DumortOrder Ambuchananiales Seppelt amp HACrum

Ambuchananiaceae Seppelt amp HACrumSubdivision Bryophytina Engler

Class Andreaeopsida JHSchaffnSubclass Andreaeidae Engl

Order Andreaeales LimprAndreaeaceae Dumort

Subclass Andreaeobryidae OchyraOrder Andreaeobryales BMMurray

Andreaeobryaceae Steere amp BMMurrayClass Oedipodiopsida Goffinet amp WRBuck

Order Oedipodiales Goffinet amp WRBuckOedipodiaceae Schimp

Class Tetraphidopsida Goffinet amp WRBuckOrder Tetraphidales MFleisch

Tetraphidaceae SchimpClass Polytrichopsida Doweld

Order Polytrichales MFleischPolytrichaceae Schwaumlgr

Class Bryopsida PaxSubclass Buxbaumiidae Doweld

Order Buxbaumiales MFleischBuxbaumiaceae Schimp

Subclass Diphysciidae OchyraOrder Diphysciales MFleisch

Diphysciaceae MFleischSubclass Timmiidae Ochyra

Order Timmiales OchyraTimmiaceae Schimp

Subclass Encalyptidae Ochyra Żarnowiec amp Bednarek-OchyraOrder Encalyptales Dixon

Encalyptaceae SchimpSubclass Funariidae Ochyra

Order Funariales MFleischFunariaceae Schwaumlgr Disceliaceae Schimp

Subclass Gigaspermidae Stech amp WFreyOrder Gigaspermales Goffinet Wickett OWerner Ros AJShaw amp CJCox

Gigaspermaceae LindbSubclass Dicranidae Doweld

Order Catoscopiales Ignatov amp IgnatovaCatoscopiaceae Broth

Order Scouleriales Goffinet amp WRBuckDrummondiaceae Goffinet Scouleriaceae SPChurchill

Order Bryoxiphiales HACrum amp LEAndersonBryoxiphiaceae Besch

16

Order Grimmiales MFleischGrimmiaceae Arn Ptychomitriaceae Schimp Seligeriaceae Schimp

Order Archidiales LimprArchidiaceae Schimp

Order Mitteniales ShawMitteniaceae Broth

Order Dicranales HPhilib ex MFleischAmphidiaceae Stech Aongstroemiaceae De Not BruchiaceaeSchimp Calymperaceae Kindb Dicranaceae Schimp Dicranel-laceae Stech Ditrichaceae Limpr Erpodiaceae Broth EustichiaceaeBroth Fissidentaceae Schimp Leucobryaceae Schimp Onco-phoraceae Stech Rhachitheciaceae HRob Schistostegaceae SchimpViridivelleraceae IGStone Wardiaceae Welch

Order Pottiales MFleischEphemeraceae Schimp Hypodontiaceae Stech PleurophascaceaeBroth Pottiaceae Schimp Serpotortellaceae WDReese amp RHZander

Subclass Bryidae EnglOrder Hedwigiales Ochyra

Hedwigiaceae Schimp Rhacocarpaceae KindbOrder Helicophyllales Stech amp WFrey

Helicophyllaceae BrothOrder Bartramiales DQuandt NEBell amp Stech

Bartramiaceae SchwaumlgrOrder Splachnales Ochyra

Meesiaceae Schimp Splachnaceae Grev amp ArnOrder Bryales Limpr

Bryaceae Schwaumlgr Leptostomataceae Schwaumlgr Mniaceae SchwaumlgrPhyllodrepaniaceae Crosby Pseudoditrichaceae Steere amp ZIwatsPulchrinodaceae DQuandt NEBell amp Stech

Order Orthotrichales DixonOrthotrichaceae Arn

Order Orthodontiales NEBell AENewton amp DQuandtOrthodontiaceae Goffinet

Order Aulacomniales NEBell AENewton amp DQuandtAulacomniaceae Schimp

Order Rhizogoniales Goffinet amp WRBuckRhizogoniaceae Broth

Order Hypnodendrales NEBell AENewton amp DQuandtBraithwaiteaceae NEBell AENewton amp DQuandt Hypnodendra-ceae Broth Pterobryellaceae WRBuck amp Vitt Racopilaceae Kindb

Order Ptychomniales WRBuck CJCox AJShaw amp GoffinetPtychomniaceae MFleisch

Order Hookeriales MFleischDaltoniaceae Schimp Hookeriaceae Schimp HypopterygiaceaeMitt Leucomiaceae Broth Pilotrichaceae Kindb SaulomataceaeWRBuck CJCox AJShaw amp Goffinet Schimperobryaceae WR

17

Buck CJCox AJShaw amp GoffinetOrder Hypnales WRBuck amp Vitt

Amblystegiaceae GRoth Anomodontaceae Kindb BrachytheciaceaeSchimp Calliergonaceae Vanderpoorten Hedenaumls CJCox amp AJShaw Catagoniaceae WRBuck amp Ireland Climaciaceae KindbCryphaeaceae Schimp Echinodiaceae Broth Entodontaceae KindbFabroniaceae Schimp Fontinalaceae Schimp Helodiaceae OchyraHeterocladiaceae Ignatov amp Ignatova Hylocomiaceae MFleischHypnaceae Schimp Lembophyllaceae Broth LeptodontaceaeSchimp Lepyrodontaceae Broth Leskeaceae Schimp Leucodon-taceae Schimp Meteoriaceae Kindb Microtheciellaceae HAMillamp AJHarr Myriniaceae Schimp Myuriaceae MFleisch NeckeraceaeSchimp Orthorrhynchiaceae SHLin Phyllogoniaceae KindbPlagiotheciaceae MFleisch Pleuroziopsidaceae Ireland Prionodon-taceae Broth Pseudoleskeaceae Schimp PseudoleskeellaceaeIgnatov amp Ignatova Pterigynandraceae Schimp PterobryaceaeKindb Pylaisiaceae Schimp Pylaisiadelphaceae Goffinet amp WRBuck Regmatodontaceae Broth Rhytidiaceae Broth RigodiaceaeHACrum Rutenbergiaceae MFleisch Scorpidiaceae Ignatov ampIgnatova Sematophyllaceae Broth Sorapillaceae MFleisch Ste-reophyllaceae WRBuck amp Ireland Symphyodontaceae MFleischTheliaceae MFleisch Thuidiaceae Schimp TrachylomataceaeWRBuck amp Vitt

Acknowledgements

Sincere thanks are due to JLReveal (Ithaca) as well as WFPrudhomme van Reine and JFVeldkamp(Leiden) for comments and discussions about suprafamilial taxonomy to DQuandt (Dresden) for providingDNA from Rhacocarpus and Bartramiaceae species and to BGiesicke (Berlin) for technical assistance

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BELL NE amp AE NEWTON (2007) Pleurocarpy in the Rhizogoniaceous grade - In NEWTONAE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolution SystematicsAssociation Special Volume Series 71 41-64

BELL NE D QUANDT TJ OBRIEN amp AE NEWTON (2007) Taxonomy and phylogeny inthe earliest diverging pleurocarps square holes and bifurcating pegs - Bryologist 110 533-560

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18

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GOFFINET B amp WR BUCK (2004) Systematics of Bryophyta (mosses) from molecules to arevised classification - In GOFFINET B V HOLLOWELL amp R MAGILL (eds) Molecularsystematics of bryophytes Monogr Syst Bot Missouri Bot Gard 98 205-239

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GOFFINET B NJ WICKETT O WERNER RM ROS AJ SHAW amp CJ COX (2007)Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae(Bryophyta) - Ann Bot 99 747-753

19

GROTH-MALONEK M D PRUCHNER F GREWE amp V KNOOP (2005) Ancestors oftrans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosseswith vascular plants - Mol Biol Evol 22 117-125

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MCNEILL J FR BARRIE HM BURDET V DEMOULIN DL HAWKSWORTHK MARHOLD DH NICOLSON J PRADO PC SILVA JE SKOG JH WIERSEMA ampNJ TURLAND (2006) International Code of Botanical Nomenclature (Vienna Code) - RegnumVegetabile 146 1-568

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MUumlLLER K D QUANDT J MUumlLLER amp C NEINHUIS (2005) PhyDE v0992 PhylogeneticData Editor - httpwwwphydede

MURRAY BM (1988) Systematics of the Andreaeopsida (Bryophyta) two orders with links toTakakia - Nova Hedwigia Beih 90 289-336

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OCHYRA R (2002) Nomenclatural changes in subfamilies of the Dicranaceae - CryptogamieBryol 23 345-349

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OCHYRA R J ŻARNOWIEC amp H BEDNAREK-OCHYRA (2003) Census catalogue ofPolish mosses - Biodiv Poland 3 1-372

PEDERSEN N amp AE NEWTON (2007) Phylogenetic and morphological studies within thePtychomniales with emphasis on the evolution of dwarf males - In NEWTON AE amp RSTANGNEY (eds) Pleurocarpous mosses systematics and evolution Systematics AssociationSpecial Volume Series 71 367-392

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21

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Received 3 September 2007 accepted in revised form 30 October 2007

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6

primers CM

DM

(slightly modified after Taberlet et al 1991 see Frey et al 1999) and atpB-1rbcL-1(Chiang et al 1998) respectively For amplification of the psbA-trnH spacer primers psbAF(5-GTT ATG CAT GAA CGT AAT GCT C-3 Sang et al 1997) and trnHR-2 (5-CGC GCA TGGTGG ATT CAC AAT CC-3 slightly modified after Sang et al 1997) were used with a PCRprotocol of 5 min 94degC 35 cycles (30 sec 94degC 1 min 48degC 1 min 40 sec 72degC) 7 min 72degC PCRproducts were purified using DNA purification kits (Qiagen Macherey-Nagel) Sequencing wasperformed as described in Stech (2004) using the amplification primers

ALIGNMENT AND PHYLOGENETIC ANALYSES DNA sequences were manually aligned in PhyDE v0992(Muumlller et al 2005) Following Quandt et al (2003) and Quandt amp Stech (2005) inversions inputative hairpin secondary structures were positionally separated in the alignment their presence orabsence was not coded for the phylogenetic analyses Phylogenetic reconstructions under the maximumparsimony criterion were performed using winPAUP 40b10 (Swofford 2002) in combination withPRAP (Muumlller 2004) as implemented in SeqState (Muumlller 2005) PRAP generates command filesfor PAUP that allow parsimony ratchet searches as designed by Nixon (1999) Heuristic searchesunder parsimony were performed with the following options all characters equally weighted andunordered TBR branch swapping collapse branches if maximum branch length is zero MulTreesoption in effect gaps treated as missing data Initially a heuristic search with 1000 addition sequencereplicates was performed For the parsimony ratchet ten random addition cycles of 200 ratchetiterations each were used with TBR branch swapping on a randomly re-weighted data set (25 ofthe positions) Heuristic bootstrap searches were performed with 1000 replicates with 10 additionsequence replicates per bootstrap replicate

Results

In the present data set of non-coding plastid markers sequence lengths ranged from243 to 368 nucleotides (nt) in the trnL intron and from 445 to 615 nt in the atpB-rbcL spacer The psbA-trnH spacer was considerably shorter than the other twomarkers and ranged from 103 to 186 nt The combined alignment of sequences from85 ingroup and two outgroup taxa comprised 2430 positions (trnL intron 668 atpB-rbcL spacer 1366 psbA-trnH spacer 396 positions) The most variable regions withambiguous alignment (781 positions) were excluded from phylogenetic analysis Ofthe 1649 included positions 628 (381) were variable and 455 of the variablepositions (725 or 276 of the total number of positions) were parsimony-informative The trnL intron comprised 124 the atpB-rbcL spacer 286 and the psbA-trnH spacer 45 of these included parsimony-informative positions

The shortest trees found in the heuristic maximum parsimony analysis of the combineddata set had a length of 2433 steps By applying the parsimony ratchet 129 treeswere retained that were one step shorter (length 2432 CI = 0419 RI = 0624) Thestrict consensus tree of the ratchet analysis is shown in Fig 1 The ingroup (Bryopsida)is supported with 100 bootstrap support (BS) Diphysciidae are sister to theremaining Bryopsida with 54 BS Encalyptidae Funariidae Timmiidae andDicranidae all receive gt 95 BS while Bryidae are slightly less supported (89BS) Relationships between these major lineages are resolved but unsupported Atordinal level within the Bryidae a lower resolution is observed SplachnalesOrthotrichales Aulacomniales Hypnodendrales Hookeriales and Hypnales areresolved as monophyletic with 67-100 BS whereas Hedwigiales BartramialesBryales Orthodontiales and Rhizogoniales are not A closer relationship ofOrthotrichales with the pleurocarpous mosses sl than with the more basal ordersHedwigiales Bartramiales Splachnales and Bryales is indicated

7

Discussion

Classification of mosses - recent progress and the current state

For a long time mosses were subdivided into three main lineages the subclassesSphagnidae Andreaeidae and Bryidae (eg Fleischer 1920 Vitt 1984 Frahm ampFrey 1987) the latter with a number of (super-)orders (eg Frey 1977) Howevermolecular data confirmed that mosses comprise a number of isolated basal lineagesrepresented by morphologically and ecologically distinct extant taxa such as TakakiaSphagnum Andreaea Andreaeobryum Oedipodium Tetraphis the Polytrichaceaeand Buxbaumia which probably have long independent phylogenetic histories (cfNewton et al 2007) As a result of molecular phylogenies and a re-evaluation ofmorphological-anatomical characters the classification of mosses has changedconsiderably in the last few years with the main lineages nowadays treated atsubdivision class and subclass levels within division Bryophyta (eg Doweld 2001Ochyra et al 2003 Goffinet amp Buck 2004 this study)

Takakia and Sphagnum are the earliest diverging moss taxa in molecular phylogenies(eg Newton et al 2000 Beckert et al 2001 Cox et al 2004 Qiu et al 2006Newton et al 2007) That Takakia is a moss and not a liverwort was confirmed byanalysis of DNA sequences and phylogenomic characters such as the distribution ofmitochondrial introns (eg Beckert et al 2001) Its taxonomic status however stillremains to be clarified On the one hand most molecular studies resolve Takakiaand Sphagnum as sister genera although only partly with high statistical supportThese molecular topologies do not support the recognition of division Takakiophytaas proposed by Crandall-Stotler (1986) One the other hand no morphologicalsynapomorphies unite Takakia with Sphagnum and significant molecular differencesseparating Takakia from all other mosses were also observed For example a regionin the plastid ITS3 is similar to that of other land plants but absent in mosses(Samigullin et al 2002) and a transition in the trnL

UAA gene changing the anticodon

to CAA was otherwise only found in leptosporangiate ferns and Ginkgo (Quandt etal 2004) Thus ldquoresolution of Sphagnum - Takakia clade may be an artifactrdquo (Shawamp Renzaglia 2004) Also Goffinet amp Buck (2004) did not unite Takakia and Sphagnumunder a formal taxonomic rank but placed them into different informal superclassesIn our opinion Takakia should be treated at the same level as Sphagnophytina andBryophytina (cf Doweld 2001) ie as a subdivision of Bryophyta However morefundamental nomenclatural changes are necessary as the family name Takakiaceaewas not validated in the original publication by Hattori amp Inoue (1958) (article411 of ICBN McNeill et al 2006) and consequently all higher taxa erected laterare invalid The corrected taxonomic treatment of Takakia is provided here withsporophytic characters included in the latin diagnosis of Takakiaceae (see taxonomy)

Within Bryophytina we recognise four morphologically and molecularly isolatedbasal lineages as separated from the arthrodontous mosses (Bryopsida) Andreaeopsida(with linear capsule dehiscence) the operculate but eperistomate Oedipodiopsida aswell as Polytrichopsida and Tetraphidopsida with nematodontous peristomes A fifthclass Andreaeobryopsida was erected by Buck amp Goffinet (2000) but re-includedin Andreaeopsida as a subclass by Ochyra et al (2003) The systematic status of

8

Andreaeobryum macrosporum Steere amp BMMurray and possible relationships withAndreaea and Takakia were discussed by Murray (1988) and summarised includingmolecular results by Shaw amp Renzaglia (2004)

On the next lower level a number of morphologically and molecularly divergentlineages are nowadays treated as subclasses of Bryopsida Buxbaumiidae andDiphysciidae are generally branching off first in molecular topologies (eg Beckertet al 2001 Magombo 2003 Cox et al 2004) followed by Timmiidae Encalyptidaeand Funariidae as well as Dicranidae (haplolepideous mosses) sister to Bryidae slThese subclasses (except Buxbaumiidae not included) are also well recognizable inthe present analysis of non-coding plastid sequences (Fig 1)

The morphologically very different Encalyptidae and Funariidae are revealed assister groups although mostly without high support in several molecular phylogenies(eg Goffinet et al 2001 Cox et al 2004 Hedderson et al 2004 Tsubota et al2003 2004) and also in the present study (Fig 1) Goffinet et al (2007) confirmedthis relationship by phylogenomic evidence namely a large (71 kb) inversion in thechloroplast genome of Funariaceae Disceliaceae and Encalyptaceae but not inGigaspermaceae Consequently the latter family was separated at ordinal level fromthe two remaining families of Funariales by Goffinet et al (2007) GigaspermalesFunariales and Encalyptales may share a common ancestor according to some butnot all molecular phylogenies (eg Goffinet et al 2001 2007 Hedderson et al2004 but not in Tsubota et al 2004) Although ontogenetic data from peristomedevelopment may support their common ancestry (Goffinet et al 2007) unambiguousmorphological synapomorphies are lacking We therefore propose to treatGigaspermaceae at subclass level within the Bryopsida (see taxonomy)

The haplolepideous mosses (Dicranidae) are clearly supported as a monophyleticlineage which obviously evolved from a diplolepideous ancestor according to theirposition in the molecular trees (eg Newton et al 2000 Tsubota et al 2003 Cox etal 2004 Goffinet amp Buck 2004) Molecular studies suitable for inferring ordinaland family level relationships within Dicranidae either focused on the haplolepideousmosses (eg Stech 1999ab 2004 LaFarge et al 2000 2002 Tsubota et al 2003Hedderson et al 2004) or included more than 15 haplolepideous taxa in analyses ofa broader range of mosses (eg Goffinet et al 2001 Tsubota et al 2004 this study)Major lineages supported by these analyses are for example Grimmiales(Grimmiaceae Ptychomitriaceae and Seligeriaceae) Leucobryaceae (incl formerDicranaceae-Campylopoideae and Paraleucobryoideae pp) Dicranaceae sstr(Dicranoideae plus former Dicnemonaceae and Paraleucobryoideae pp) Pottiaceae(incl Cinclidotaceae and Splachnobryum) and Calymperaceae (probably exclOctoblepharum) Furthermore several genera and families belong to Dicranidaewhose systematic positions have been controversial (eg Stech et al 1999b LaFarge et al 2002 Hedderson et al 2004 OBrien 2007 Quandt et al 2007 thisstudy) Amphidium Archidium Catoscopium Drummondia EphemeraceaeErpodiaceae Mittenia (cf OBrien 2007 sequences in some earlier analyses werebased on misdentified specimens) Rhachitheciaceae Schistostega Splachnobryumand Wardia On the contrary several problems remain such as the circumscriptionof Ditrichaceae and relationships of the major haplolepideous lineages in general

9

Fig 1 Strict consensus tree of 129 most parsimonious trees inferred from combined trnLUAA

intronatpB-rbcL spacer and psbA-trnH spacer sequences of 85 taxa of Bryopsida as well as Andreaearupestris (Andreaeopsida) and Pogonatum subulatum (Polytrichopsida) as outgroup representativesBootstrap support values gt50 are depicted above the branches

10

Consequently resolving the phylogeny of Dicranidae with confidence is one of themajor future challenges in moss systematics

As mentioned above Dicranaceae are monophyletic in a narrow circumscriptionaccording to molecular data In contrast to former Campylopoideae andParaleucobryoideae the status of Rhabdoweisioideae (= Oncophoroideae Ochyra2002) and Dicranelloideae needs further consideration Stech (1999ab) suggestedto recognise RhabdoweisioideaeRhabdoweisiaceae in a broad sense includingDicranoweisia Amphidium and Aongstroemia Subsequent molecular analysesconfirmed a close relationship of the genera Arctoa Cynodontium DicranoweisiaKiaeria Oncophorus Oreoweisia Oreas Rhabdoweisia and Symblepharis althoughwithout significant support (La Farge et al 2002 Tsubota et al 2003 Hedderson etal 2004) With respect to the molecular evidence available so far we propose toelevate Oncophoroideae to family level to accomodate these genera and perhapsGlyphomitrium (cf Tsubota et al 2003) whereas we consider AongstroemiaDichodontium and Diobelonella to belong to Aongstroemiaceae (cf Stech 1999a)Amphidium is neither closely related to Dicranaceae sstr nor to Oncophoroideae(La Farge et al 2002 Tsubota et al 2003 Hedderson et al 2004 Stech 2004 thisstudy) and should be treated at family level rather than placed in Dicranaceae assubfam Amphidioideae (Ochyra et al 2003) The circumscription of Dicranelloideaeis more difficult to evaluate as few representatives have been included in molecularanalyses However Dicranella heteromalla (Hedw) Schimp as well as the generaCampylopodium and Microcampylopus are clearly separated from Dicranaceae sstr(Stech 1999a 2004 La Farge et al 2002 Tsubota et al 2003 Hedderson et al2004) and consequently the subfamily deserves family status as well Finallymolecular data showed that the genus Hypodontium does not belong to Pottiaceae(Hedderson et al 2004 Tsubota et al 2004) Taxonomic conclusions have not beendrawn from these results which is made up here (see taxonomy)

All mosses with diplolepideous-alternate peristomes together with Splachnales witha diplolepideous-opposite (Funaria-type) peristome form a monophyletic group inmolecular analyses (eg Newton et al 2000 Beckert et al 2001 Goffinet et al2001 Cox et al 2004 Tsubota et al 2004 references in Table 2) Differentclassifications of this by far most species-rich group of mosses were proposed (egVitt et al 1998 Ochyra et al 2003 Goffinet amp Buck 2004) However at least someof the recognised subclasses and superorders are paraphyletic according to themolecular topologies and assigning formal ranks to all evolutionarily significantmonophyletic entities is problematic if the main taxonomic framework of Bryophytaand Bryopsida should be maintained (cf discussion in Bell et al 2007) Thereforein the present synopsis only one subclass Bryidae is recognised for all diplolepideous-alternate mosses and Splachnales This broadly defined Bryidae is subdivided into13 orders most of them resolved as monophyletic in the majority of the phylogeneticanalyses summarised in Table 2 although with different levels of statistical supportin maximum parsimony analyses To define monophyletic lineages at supraordinallevel informal node-based names may be chosen according to Bell et al (2007) Forexample the pleurocarpous mosses (pleurocarpy sensu Bell amp Newton 2007) andtheir closest acrocarpous relatives (Orthodontiales to Hypnales) were already

11

Table 2 Taxon sampling and bootstrap support (BS) for Dicranidae Bryidae and orders within theBryidae in recent phylogenetic analyses (MP only) based on combined molecular markers Markersare given in square brackets (non-coding regions in bold) numbers of included taxa in brackets ++respective clade present with ge 80 BS + clade present with lt 80 BS - clade not present no oronly one representative included

Bell amp Newton OBrien Quandt et al Bell et al this study(2004) (2007) (2007) (2007)

[rbcL rps4 [atpB atpB- [rbcL rps4 [rbcL rps4 [atpB-rbcLnad5] rbcL rbcL trnL-F nad5] trnL-F nad5] psbA-trnH

rps4 trnL-F] trnL]

Dicranidae + (2) + (4) ++ (3) (1) ++ (19)Bryidae ++ (57) + (53) ++ (52) ++ (98) ++ (58)Hedwigiales ++ (2) (1) ++ (2) ++ (2) - (3)Bartramiales ++ (2) ++ (4) ++ (4) ++ (3) - (4)Splachnales (0) ++ (2) ++ (3) ++ (2) ++ (5)Bryales - (4) - (5) ++ (18) + (17) - (8)Orthotrichales (1) ++ (3) ++ (3) ++ (2) ++ (4)Orthodontiales + (4) + (4) + (3) + (6) - (3)Aulacomniales + (6) + (7) ++ (2) + (7) + (3)Rhizogoniales ++ (13) + (8) ++ (5) ++ (14) - (3)Hypnodendrales ++ (13) + (7) ++ (4) ++ (29) ++ (6)Ptychomniales ++ (3) ++ (3) (1) ++ (4) (1)Hookeriales - (4) + (2) (1) + (2) + (8)Hypnales - (5) - (7) ++ (5) ++ (10) + (10)

summarised under the informal node based name pleurcarpids (Bell et al 2007)and can be distinguished from a basal grade of acrocarpous or cladocarpous lineages(Hedwigiales to Orthotrichales) Within the latter monophyly of BartramialesSplachnales and Orthotrichales is well-supported in all analyses including two ormore taxa except Bartramiales in the present data set (cf Fig 1) In contrast Bryalesreceive significant support less frequently (but see Bell et al 2007 Quandt et al2007) Hedwigiales are well supported if only Hedwigia (Hedwigiaceae) andRhacocarpus (Rhacocarpaceae) are included whereas the monospecific Helicophyllum(Helicophyllaceae) is not closely related to these taxa but shows affinities withBartramiales (Goffinet et al 2001 this study) With respect to the differentmorphologies of Helicophyllaceae and Bartramiaceae however the former shouldbe separated at ordinal level (see taxonomy)

Clarifying relationships of the Orthotrichales is still a difficult issue Analyses ofsingle chloroplast markers or parsimony analyses of combined markers from differentgenomes mostly indicated a close relationship either with Splachnales (eg Cox etal 2000 Newton et al 2000 Tsubota et al 2004 Quandt et al 2007) or with thepleurocarpids (Goffinet et al 2001 this study) Although none of these alternativesis well-supported the latter seems more likely with regard to the moderately tomaximally supported Orthotrichales - pleurocarpid sister group relationship in allanalyses of mitochondrial data and in likelihood analyses of combined plastidmitochondrial markers (Beckert et al 2001 Quandt et al 2007)

12

The molecular polyphyly of Rhizogoniaceae (eg Bell amp Newton 2004) was solvedby the transfer of rhizogonioid genera into broadly defined Aulacomniaceae andOrthodontiaceae (Bell et al 2007) which now include both acrocarpous andpleurocarpous taxa These systematic changes are also comprehensible by non-molecular characters such as morphological traits shared by Mesochaete andAulacomnium heterostichum (Hedw) Bruch amp Schimp or the variously reducedperistomes of Orthodontiaceae pp in contrast to the generally fully developed Bryum-type peristomes of rhizogonioid and hypnodendroid mosses (Bell et al 2007) Theposition of the solely pleurocarpous Hypnodendrales sister to the former Hypnidaeled to the recognition of the informal group core pleurocarps (Bell et al 2007)The former Hypnidae (Ptychomniales Hookeriales and Hypnales summarised ashomocostate pleurocarps) are monophyletic in most molecular analyses (eg Goffinetet al 2001 Tsubota et al 2004 Bell et al 2007) with Ptychomniales being well-supported (Pedersen amp Newton 2007 Table 2) Clarifying relationships betweenHookeriales and Hypnales and within the latter is still a challenge but recent molecularstudies seem to support a sister group relationship of both orders (Bell et al 2007present study)

Phylogenetic utility of non-coding plastid markers

Non-coding plastid markers that comprise both variable and conserved regionssuch as the trnL

UAA intron have repeatedly been shown to possess potential for

resolving relationships at high taxonomic levels (eg Borsch et al 2003 Quandtet al 2004) Both the trnL intron and atpB-rbcL spacer were characterised indetail in mosses with respect to their structure and molecular evolution (Quandt ampStech 2005 Stech amp Quandt 2006) They include conservative regions that can beunambiguosly aligned and even parts of the more variable regions can be used ifrepeats hairpin loops etc are correctly identified and adequately treated in thephylogenetic analyses (eg Quandt et al 2003 Quandt amp Stech 2005) Using theatpB-rbcL spacer alone (Stech amp Quandt 2006) relationships of the major mosslineages were largely consistent with the ldquototal evidencerdquo molecular tree of Goffinetamp Buck (2004) However in addition to general limitations that result from singlemarker analyses the use of non-coding markers may pose further problems suchas a high amount of homoplasy resulting in low resolution or low statistical supportfor many clades Therefore several recent molecular studies of relationships withinBryidae have employed both coding and non-coding markers (Table 2)Nevertheless the usefulness of analyses of combined non-coding plastid markerscannot be ruled out In fact Fig 1 and Table 2 indicate a phylogenetic signal inthe present data set as many clades are recovered that are usually also resolvedin analyses of coding or combined coding and non-coding markers Especiallywith regard to statistical support however the present analysis is inferior tothose of other recent data sets especially Bell et al (2007) and Quandt et al(2007) In addition the non-coding markers used here are of different suitabilityand even the two intergenic spacers differ considerably from each other ThepsbA-trnH spacer contributes much less to the trees resolution than the atpB-rbcL spacer first because it is much shorter and second because relatively largeparts are attributed to hairpin loops or otherwise hypervariable regions These

13

results indicate that future studies should evaluate the molecular evolution andphylogenetic potential of new markers both coding and con-coding and choosethe most suitable ones in a combined analysis to resolve the remaining uncertaintiesin moss phylogeny

Taxonomy

Takakiaceae Stech amp WFrey stat nov

Plantae virides nusquam rhizophorae sine protonemate e caudicis rhizomatis erectae Caudicesrhizomati et axes geotropi radiformes frequenter intercalariter ramificantes sine phyllidiis cumpapillis mucilaginis rostratis Caules phyllidiiferi saepe furcati Phyllidia sine lamina et costadistincta profunde 2-4(-5)-lobata pluristratosa tristicha sed torsione spiraliter disposita Filumcentralium in ambabus generationibus (axibus gametophyti et setis) adest Plantae dioicae Antheridiaet archegonia nuda Sporophytum terminale solitarium Seta persistens Capsula tortilis admaturitatem schizocarpa secus unam rimam spiralem longitudinalem dehiscens Stomata etoperculum absunt peristomium nullum Calyptra mitriformis

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiaceae SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval (Art 411)

Takakiales Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiales SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval

Takakiales SHatt amp Inoue ex RMSchust J Hattori Bot Lab 26 224 1963 nom inval (cumdescr latin)

Takakiopsida Stech amp WFrey statnov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiopsida Goffinet amp WRBuck Monogr Syst Bot Missouri Bot Gard 98 232 2004 nominval

Takakiopsida Jia et al Acta Phytotax Sin 41 350 351 2003 nom nud

Takakiopsida Wang amp Wu Fl Bryophyt Sin 8 447 2004 nom inval (cum descr latin)

Takakiophytina Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue JHattori Bot Lab 19 137 1958

Gigaspermidae Stech amp WFrey subclass nov

Plantae acrocarpae terrestres stoloniferae ramis brevibus erectis Folia unicostata cellulis laxislaevibus Capsula plerumque valde rugosa gymnostomatica vel cleistocarpa stomata cum duabuscellulis sociis Ab Funariidis et Encalyptidis charactere phylogenomico (71-kb inversio abest)separatae

14

TYPUS Gigaspermum Lindb Oumlfversigt af Foumlrhandlingar Kongl Svenska Vetenskaps-Akademien21 599 1865

Amphidiaceae Stech stat nov

Based on Dicranaceae subfam Amphidioideae Ochyra in Ochyra Zarnowiec amp Bednarek-OchyraCens Cat Polish Mosses 110 2003

TYPUS Amphidium Schimp Coroll Bryol Eur 39 1856

Amphidiaceae AJESm Moss Fl Britain Ireland 2nd ed 657 2004 nom inval descr angl

Dicranellaceae Stech stat nov

Based on Dicranaceae subfam Dicranelloideae Lindb Utkast Eur Bladmoss 33 1878[lsquoUnderfamilje Dicranelleaersquo]

TYPUS Dicranella (MuumlllHal) Schimp Coroll Bryol Eur 13 1856

Oncophoraceae Stech stat nov

Based on Dicranaceae subfam Oncophoroideae Lindb Utkast Eur Bladmoss 34 1878[lsquoUnderfamilje Oncophoreaersquo]

TYPUS Oncophorus (Brid) Brid Bryol Univ 1 389 1826

Hypodontiaceae Stech fam nov

Plantae robustae characteribus morphologicis Pottiaceis et Calymperaceis similes sedcharacteribus molecularicis separatae Bracteae perichaetiales internae e basi vaginantes subulataevel aristatae Capsula aspectu succulenta cellulae exothecii incrassatae annulus magnopereabsens Peristomii dentes breves triangulati incurvati aurantiaci leves vel infirme verrucosiCalyptra cucullata

TYPUS Hypodontium MuumlllHal Hedwigia 38 96 1899

Helicophyllales Stech amp WFrey ord nov

Plantae acrocarpae prostratae tomentosae Folia dimorpha in duas series laterales et unam seriemventralem divisa Costa percurrens Cellulae hexagonae ad subquadratae papillosae Capsula immersacupulata ad oblonga infra orificium abrupte incurvata stomata destituta Peristomium nullum Sporaeisomorphae heteropolares granulatae

TYPUS Helicophyllum Brid Bryol Univ 2 771 1827

Synopsis of the suprageneric classification of BryophytaAuthor citations are in accordance with Art 492 of the Vienna Code (McNeill et al 2006)

Subdivision Takakiophytina Stech amp WFreyClass Takakiopsida Stech amp WFrey

Order Takakiales Stech amp WFreyTakakiaceae Stech amp WFrey

Subdivision Sphagnophytina DoweldClass Sphagnopsida Schimp

Order Sphagnales Limpr

15

Sphagnaceae DumortOrder Ambuchananiales Seppelt amp HACrum

Ambuchananiaceae Seppelt amp HACrumSubdivision Bryophytina Engler

Class Andreaeopsida JHSchaffnSubclass Andreaeidae Engl

Order Andreaeales LimprAndreaeaceae Dumort

Subclass Andreaeobryidae OchyraOrder Andreaeobryales BMMurray

Andreaeobryaceae Steere amp BMMurrayClass Oedipodiopsida Goffinet amp WRBuck

Order Oedipodiales Goffinet amp WRBuckOedipodiaceae Schimp

Class Tetraphidopsida Goffinet amp WRBuckOrder Tetraphidales MFleisch

Tetraphidaceae SchimpClass Polytrichopsida Doweld

Order Polytrichales MFleischPolytrichaceae Schwaumlgr

Class Bryopsida PaxSubclass Buxbaumiidae Doweld

Order Buxbaumiales MFleischBuxbaumiaceae Schimp

Subclass Diphysciidae OchyraOrder Diphysciales MFleisch

Diphysciaceae MFleischSubclass Timmiidae Ochyra

Order Timmiales OchyraTimmiaceae Schimp

Subclass Encalyptidae Ochyra Żarnowiec amp Bednarek-OchyraOrder Encalyptales Dixon

Encalyptaceae SchimpSubclass Funariidae Ochyra

Order Funariales MFleischFunariaceae Schwaumlgr Disceliaceae Schimp

Subclass Gigaspermidae Stech amp WFreyOrder Gigaspermales Goffinet Wickett OWerner Ros AJShaw amp CJCox

Gigaspermaceae LindbSubclass Dicranidae Doweld

Order Catoscopiales Ignatov amp IgnatovaCatoscopiaceae Broth

Order Scouleriales Goffinet amp WRBuckDrummondiaceae Goffinet Scouleriaceae SPChurchill

Order Bryoxiphiales HACrum amp LEAndersonBryoxiphiaceae Besch

16

Order Grimmiales MFleischGrimmiaceae Arn Ptychomitriaceae Schimp Seligeriaceae Schimp

Order Archidiales LimprArchidiaceae Schimp

Order Mitteniales ShawMitteniaceae Broth

Order Dicranales HPhilib ex MFleischAmphidiaceae Stech Aongstroemiaceae De Not BruchiaceaeSchimp Calymperaceae Kindb Dicranaceae Schimp Dicranel-laceae Stech Ditrichaceae Limpr Erpodiaceae Broth EustichiaceaeBroth Fissidentaceae Schimp Leucobryaceae Schimp Onco-phoraceae Stech Rhachitheciaceae HRob Schistostegaceae SchimpViridivelleraceae IGStone Wardiaceae Welch

Order Pottiales MFleischEphemeraceae Schimp Hypodontiaceae Stech PleurophascaceaeBroth Pottiaceae Schimp Serpotortellaceae WDReese amp RHZander

Subclass Bryidae EnglOrder Hedwigiales Ochyra

Hedwigiaceae Schimp Rhacocarpaceae KindbOrder Helicophyllales Stech amp WFrey

Helicophyllaceae BrothOrder Bartramiales DQuandt NEBell amp Stech

Bartramiaceae SchwaumlgrOrder Splachnales Ochyra

Meesiaceae Schimp Splachnaceae Grev amp ArnOrder Bryales Limpr

Bryaceae Schwaumlgr Leptostomataceae Schwaumlgr Mniaceae SchwaumlgrPhyllodrepaniaceae Crosby Pseudoditrichaceae Steere amp ZIwatsPulchrinodaceae DQuandt NEBell amp Stech

Order Orthotrichales DixonOrthotrichaceae Arn

Order Orthodontiales NEBell AENewton amp DQuandtOrthodontiaceae Goffinet

Order Aulacomniales NEBell AENewton amp DQuandtAulacomniaceae Schimp

Order Rhizogoniales Goffinet amp WRBuckRhizogoniaceae Broth

Order Hypnodendrales NEBell AENewton amp DQuandtBraithwaiteaceae NEBell AENewton amp DQuandt Hypnodendra-ceae Broth Pterobryellaceae WRBuck amp Vitt Racopilaceae Kindb

Order Ptychomniales WRBuck CJCox AJShaw amp GoffinetPtychomniaceae MFleisch

Order Hookeriales MFleischDaltoniaceae Schimp Hookeriaceae Schimp HypopterygiaceaeMitt Leucomiaceae Broth Pilotrichaceae Kindb SaulomataceaeWRBuck CJCox AJShaw amp Goffinet Schimperobryaceae WR

17

Buck CJCox AJShaw amp GoffinetOrder Hypnales WRBuck amp Vitt

Amblystegiaceae GRoth Anomodontaceae Kindb BrachytheciaceaeSchimp Calliergonaceae Vanderpoorten Hedenaumls CJCox amp AJShaw Catagoniaceae WRBuck amp Ireland Climaciaceae KindbCryphaeaceae Schimp Echinodiaceae Broth Entodontaceae KindbFabroniaceae Schimp Fontinalaceae Schimp Helodiaceae OchyraHeterocladiaceae Ignatov amp Ignatova Hylocomiaceae MFleischHypnaceae Schimp Lembophyllaceae Broth LeptodontaceaeSchimp Lepyrodontaceae Broth Leskeaceae Schimp Leucodon-taceae Schimp Meteoriaceae Kindb Microtheciellaceae HAMillamp AJHarr Myriniaceae Schimp Myuriaceae MFleisch NeckeraceaeSchimp Orthorrhynchiaceae SHLin Phyllogoniaceae KindbPlagiotheciaceae MFleisch Pleuroziopsidaceae Ireland Prionodon-taceae Broth Pseudoleskeaceae Schimp PseudoleskeellaceaeIgnatov amp Ignatova Pterigynandraceae Schimp PterobryaceaeKindb Pylaisiaceae Schimp Pylaisiadelphaceae Goffinet amp WRBuck Regmatodontaceae Broth Rhytidiaceae Broth RigodiaceaeHACrum Rutenbergiaceae MFleisch Scorpidiaceae Ignatov ampIgnatova Sematophyllaceae Broth Sorapillaceae MFleisch Ste-reophyllaceae WRBuck amp Ireland Symphyodontaceae MFleischTheliaceae MFleisch Thuidiaceae Schimp TrachylomataceaeWRBuck amp Vitt

Acknowledgements

Sincere thanks are due to JLReveal (Ithaca) as well as WFPrudhomme van Reine and JFVeldkamp(Leiden) for comments and discussions about suprafamilial taxonomy to DQuandt (Dresden) for providingDNA from Rhacocarpus and Bartramiaceae species and to BGiesicke (Berlin) for technical assistance

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BELL NE amp AE NEWTON (2004) Systematic studies of non-hypnanaean pleurocarps establishinga phylogenetic framework for investigating the origins of pleurocarpy - In GOFFINET BV HOLLOWELL amp R MAGILL (eds) Molecular systematics of bryophytes Monogr Syst BotMissouri Bot Gard 98 290-319

BELL NE amp AE NEWTON (2007) Pleurocarpy in the Rhizogoniaceous grade - In NEWTONAE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolution SystematicsAssociation Special Volume Series 71 41-64

BELL NE D QUANDT TJ OBRIEN amp AE NEWTON (2007) Taxonomy and phylogeny inthe earliest diverging pleurocarps square holes and bifurcating pegs - Bryologist 110 533-560

BORSCH T KW HILU D QUANDT V WILDE C NEINHUIS amp W BARTHLOTT(2003) Non-coding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms- J Evol Biol 16 558-576

18

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FREY W (1977) Neue Vorstellungen uumlber die Verwandtschaftsgruppen und die Stammesgeschichteder Laubmoose - In FREY W H HURKA amp F OBERWINKLER (Hrsg) Beitraumlge zur Biologieder Pflanzen pp 117-139 Stuttgart

FREY W amp M STECH (2005) A morpho-molecular classification of the liverworts (Hepa-ticophytina Bryophyta) - Nova Hedwigia 81 55-78

FREY W M STECH amp K MEIszligNER (1999) Chloroplast DNA-relationship in palaeoaustralLopidium concinnum (Hypopterygiaceae Musci) An example of steno-evolution in mosses Studiesin austral temperate rain forest bryophytes 2 - Plant Syst Evol 218 67-75

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GOFFINET B CJ COX AJ SHAW amp TAJ HEDDERSON (2001) The Bryophyta (mosses)Systematic and evolutionary inferences from an rps4 gene (cpDNA) phylogeny - Ann Bot 87191-208

GOFFINET B NJ WICKETT O WERNER RM ROS AJ SHAW amp CJ COX (2007)Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae(Bryophyta) - Ann Bot 99 747-753

19

GROTH-MALONEK M D PRUCHNER F GREWE amp V KNOOP (2005) Ancestors oftrans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosseswith vascular plants - Mol Biol Evol 22 117-125

HATTORI S amp H INOUE (1958) Preliminary report on Takakia lepidozioides - J Hattori BotLab 19 133-137

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LA FARGE C BD MISHER JA WHEELER DP WALL K JOHANNES S SCHAFFERamp AJ SHAW (2000) Phylogenetic relationships within the haplolepideous mosses - Bryologist103 257-276

LA FARGE C AJ SHAW amp DH VITT (2002) The circumscription of the Dicranaceae(Bryopsida) based on the chloroplast regions trnL-trnF and rps4 - Syst Bot 27 435-452

MAGOMBO ZLK (2003) The phylogeny of basal peristomate mosses evidence from cpDNAand implications for peristome evolution - Syst Bot 28 24-38

MCNEILL J FR BARRIE HM BURDET V DEMOULIN DL HAWKSWORTHK MARHOLD DH NICOLSON J PRADO PC SILVA JE SKOG JH WIERSEMA ampNJ TURLAND (2006) International Code of Botanical Nomenclature (Vienna Code) - RegnumVegetabile 146 1-568

MUumlLLER K (2004) PRAP - computation of Bremer support for large data sets - Mol PhylogenetEvol 31 780-782

MUumlLLER K (2005) SeqState - primer design and sequence statistics for phylogenetic DNA datasets - Appl Bioinformatics 4 65-69

MUumlLLER K D QUANDT J MUumlLLER amp C NEINHUIS (2005) PhyDE v0992 PhylogeneticData Editor - httpwwwphydede

MURRAY BM (1988) Systematics of the Andreaeopsida (Bryophyta) two orders with links toTakakia - Nova Hedwigia Beih 90 289-336

NEWTON AE amp RS TANGNEY (eds) (2007) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 CRC Press Boca Raton 434 pp

NEWTON AE CJ COX JG DUCKETT JA WHEELER B GOFFINET TAJ HEDDER-SON amp BD MISHLER (2000) Evolution of the major moss lineages Phylogenetic analyses basedon multiple gene sequences and morphology - Bryologist 103 187-211

NEWTON AE N WIKSTROumlM NE BELL LL FORREST amp MS IGNATOV (2007)Dating the diversification of the pleurocarpous mosses - In NEWTON AE amp RS TANGNEY(eds) Pleurocarpous mosses systematics and evolution Systematics Association Special VolumeSeries 71 337-366

NIXON KC (1999) The parsimony ratchet a new method for rapid parsimony analysis - Cladistics15 407-411

OBRIEN TJ (2007) The phylogenetic distribution of pleurocarpous mosses evidence fromcpDNA sequences - In NEWTON AE amp RS TANGNEY (eds) Pleurocarpous mossessystematics and evolution Systematics Association Special Volume Series 71 19-41

OCHYRA R (2002) Nomenclatural changes in subfamilies of the Dicranaceae - CryptogamieBryol 23 345-349

20

OCHYRA R J ŻARNOWIEC amp H BEDNAREK-OCHYRA (2003) Census catalogue ofPolish mosses - Biodiv Poland 3 1-372

PEDERSEN N amp AE NEWTON (2007) Phylogenetic and morphological studies within thePtychomniales with emphasis on the evolution of dwarf males - In NEWTON AE amp RSTANGNEY (eds) Pleurocarpous mosses systematics and evolution Systematics AssociationSpecial Volume Series 71 367-392

QUANDT D amp M STECH (2005) Molecular evolution and secondary structure of the chloroplasttrnL intron in bryophytes - Mol Phylogenet Evol 36 429-443

QUANDT D K MUumlLLER amp S HUTTUNEN (2003) Characterisation of the chloroplast DNApsbT-H region and the influence of dyad symmetrical elements on phylogenetic reconstructions -Plant Biol 5 400-410

QUANDT D K MUumlLLER M STECH W FREY KW HILU amp T BORSCH (2004) Molecularevolution of the chloroplast trnL-F-region in land plants - In GOFFINET B V HOLLOWELL ampR MAGILL (eds) Molecular systematics of bryophytes Monogr Syst Bot Missouri Bot Gard98 13-37

QUANDT D NE BELL amp M STECH (2007) Unravelling the knot the Pulchrinodaceae famnov (Bryales) - In KUumlRSCHNER H T PFEIFFER amp M STECH (eds) A Festschrift to Wolf-gang Frey - a scientists life between deserts and rain forests Nova Hedwigia Beih 131 21-39

QIU Y-L Y CHO JC COX amp JD PALMER (1998) The gain of three mitochondrial intronsidentifies liverworts as the earliest land plants - Nature 394 671-674

QIU Y-L L LI B WANG Z CHEN V KNOOP M GROTH-MALONEK O DOM-BROVSKA J LEE L KENT J REST GF ESTABROOK TA HENDRY DW TAYLORCM TESTA M AMBROS B CRANDALL-STOTLER J DUFF M STECH W FREYD QUANDT amp CC DAVIS (2006) The deepest divergences in land plants inferred fromphylogenomic evidence - Proc Natl Acad Sci USA 103 15511-15516

RENZAGLIA KS S SCHUETTE RJ DUFF R LIGRONE AJ SHAW BD MISHLER ampJG DUCKETT (2007) Bryophyte phylogeny Advancing the molecular and morphological frontiers- Bryologist 110 179-213

SAMIGULLIN TH SP YACENTYUK GV DEGTYARYEVA KM VALIEJO-ROMANVK BOBROVA I CAPESIUS WF MARTIN AV TROITSKY VR FILIN amp ASANTONOV (2002) Paraphyly of bryophytes and close relationships of hornworts and vascularplants inferred from analysis of chloroplast rDNA ITS (cpITS) sequences - Arctoa 11 31-43

SANG T DJ CRAWFORD amp TF STUESSY (1997) Chloroplast DNA phylogeny reticulateevolution and biogeography of Paeonia (Paeoniaceae) - Amer J Bot 84 1120-1136

SHAW AJ amp KS RENZAGLIA (2004) Phylogeny and diversification of bryophytes - AmerJ Bot 91 1557-1581

SHAW AJ CJ COX amp B GOFFINET (2005) Global patterns of moss diversity taxonomic andmolecular inferences - Taxon 54 337-352

STECH M (1999a) A reclassification of Dicranaceae (Bryopsida) based on non-coding cpDNAsequence data - J Hattori Bot Lab 86 137-159

STECH M (1999b) A molecular systematic contribution to the position of Amphidium Schimp(Rhabdoweisiaceae Bryopsida) - Nova Hedwigia 68 291-300

STECH M (2004) Supraspecific circumscription and classification of Campylopus Brid(Dicranaceae Bryopsida) based on molecular data - Syst Bot 29 817-824

STECH M amp D QUANDT (2006) Molecular evolution of the chloroplast atpB-rbcL spacer inbryophytes - In SHARMA AK amp A SHARMA (eds) Plant Genome Biodiversity and EvolutionVol 2 Part B pp 409-431 Science Publishers Enfield New Hampshire

21

STECH M D QUANDT amp W FREY (2003) Molecular circumscription of the hornworts(Antho-cerotophyta) based on the chloroplast DNA trnL-trnF region - J Plant Res 116 389-398

STOTLER RE amp B CRANDALL-STOTLER (2005) A revised classification of theAnthocerotophyta and a checklist of the hornworts of North America north of Mexico - Bryologist108 16-26

SWOFFORD DL (2002) PAUP Phylogenetic analysis using parsimony (and other methods)version 40b10 - Sunderland MA

TABERLET P L GIELLY G PAUTOU amp J BOUVET (1991) Universal primers for amplificationof three non-coding regions of chloroplast DNA - Plant Mol Biol 17 1105-1109

TSUBOTA H Y AGENO B ESTEacuteBANEZ T YAMAGUCHI amp H DEGUCHI (2003)Molecular phylogeny of the Grimmiales (Musci) based on chloroplast rbcL sequences - Hikobia 1455-70

TSUBOTA H E DE LUNA D GONZAacuteLEZ MS IGNATOV amp H DEGUCHI (2004) Molecularphylogenetics and ordinal relationships based on analyses of a large-scale data set of 600 rbcLsequences of mosses - Hikobia 14 149-170

VITT DH (1984) Classification of the Bryopsida - In SCHUSTER RM (ed) New Manual ofBryology 2 696-759 Hattori Botanical Laboratory Nichinan Japan

VITT DH B GOFFINET amp T HEDDERSON (1998) 8 The ordinal classification of the mossesquestions and answers for the 1990s - In BATES JW NW ASHTON amp JG DUCKETT (eds)Bryology for the twenty-first century British Bryol Soc pp 113-123

Received 3 September 2007 accepted in revised form 30 October 2007

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6

primers CM

DM

(slightly modified after Taberlet et al 1991 see Frey et al 1999) and atpB-1rbcL-1(Chiang et al 1998) respectively For amplification of the psbA-trnH spacer primers psbAF(5-GTT ATG CAT GAA CGT AAT GCT C-3 Sang et al 1997) and trnHR-2 (5-CGC GCA TGGTGG ATT CAC AAT CC-3 slightly modified after Sang et al 1997) were used with a PCRprotocol of 5 min 94degC 35 cycles (30 sec 94degC 1 min 48degC 1 min 40 sec 72degC) 7 min 72degC PCRproducts were purified using DNA purification kits (Qiagen Macherey-Nagel) Sequencing wasperformed as described in Stech (2004) using the amplification primers

ALIGNMENT AND PHYLOGENETIC ANALYSES DNA sequences were manually aligned in PhyDE v0992(Muumlller et al 2005) Following Quandt et al (2003) and Quandt amp Stech (2005) inversions inputative hairpin secondary structures were positionally separated in the alignment their presence orabsence was not coded for the phylogenetic analyses Phylogenetic reconstructions under the maximumparsimony criterion were performed using winPAUP 40b10 (Swofford 2002) in combination withPRAP (Muumlller 2004) as implemented in SeqState (Muumlller 2005) PRAP generates command filesfor PAUP that allow parsimony ratchet searches as designed by Nixon (1999) Heuristic searchesunder parsimony were performed with the following options all characters equally weighted andunordered TBR branch swapping collapse branches if maximum branch length is zero MulTreesoption in effect gaps treated as missing data Initially a heuristic search with 1000 addition sequencereplicates was performed For the parsimony ratchet ten random addition cycles of 200 ratchetiterations each were used with TBR branch swapping on a randomly re-weighted data set (25 ofthe positions) Heuristic bootstrap searches were performed with 1000 replicates with 10 additionsequence replicates per bootstrap replicate

Results

In the present data set of non-coding plastid markers sequence lengths ranged from243 to 368 nucleotides (nt) in the trnL intron and from 445 to 615 nt in the atpB-rbcL spacer The psbA-trnH spacer was considerably shorter than the other twomarkers and ranged from 103 to 186 nt The combined alignment of sequences from85 ingroup and two outgroup taxa comprised 2430 positions (trnL intron 668 atpB-rbcL spacer 1366 psbA-trnH spacer 396 positions) The most variable regions withambiguous alignment (781 positions) were excluded from phylogenetic analysis Ofthe 1649 included positions 628 (381) were variable and 455 of the variablepositions (725 or 276 of the total number of positions) were parsimony-informative The trnL intron comprised 124 the atpB-rbcL spacer 286 and the psbA-trnH spacer 45 of these included parsimony-informative positions

The shortest trees found in the heuristic maximum parsimony analysis of the combineddata set had a length of 2433 steps By applying the parsimony ratchet 129 treeswere retained that were one step shorter (length 2432 CI = 0419 RI = 0624) Thestrict consensus tree of the ratchet analysis is shown in Fig 1 The ingroup (Bryopsida)is supported with 100 bootstrap support (BS) Diphysciidae are sister to theremaining Bryopsida with 54 BS Encalyptidae Funariidae Timmiidae andDicranidae all receive gt 95 BS while Bryidae are slightly less supported (89BS) Relationships between these major lineages are resolved but unsupported Atordinal level within the Bryidae a lower resolution is observed SplachnalesOrthotrichales Aulacomniales Hypnodendrales Hookeriales and Hypnales areresolved as monophyletic with 67-100 BS whereas Hedwigiales BartramialesBryales Orthodontiales and Rhizogoniales are not A closer relationship ofOrthotrichales with the pleurocarpous mosses sl than with the more basal ordersHedwigiales Bartramiales Splachnales and Bryales is indicated

7

Discussion

Classification of mosses - recent progress and the current state

For a long time mosses were subdivided into three main lineages the subclassesSphagnidae Andreaeidae and Bryidae (eg Fleischer 1920 Vitt 1984 Frahm ampFrey 1987) the latter with a number of (super-)orders (eg Frey 1977) Howevermolecular data confirmed that mosses comprise a number of isolated basal lineagesrepresented by morphologically and ecologically distinct extant taxa such as TakakiaSphagnum Andreaea Andreaeobryum Oedipodium Tetraphis the Polytrichaceaeand Buxbaumia which probably have long independent phylogenetic histories (cfNewton et al 2007) As a result of molecular phylogenies and a re-evaluation ofmorphological-anatomical characters the classification of mosses has changedconsiderably in the last few years with the main lineages nowadays treated atsubdivision class and subclass levels within division Bryophyta (eg Doweld 2001Ochyra et al 2003 Goffinet amp Buck 2004 this study)

Takakia and Sphagnum are the earliest diverging moss taxa in molecular phylogenies(eg Newton et al 2000 Beckert et al 2001 Cox et al 2004 Qiu et al 2006Newton et al 2007) That Takakia is a moss and not a liverwort was confirmed byanalysis of DNA sequences and phylogenomic characters such as the distribution ofmitochondrial introns (eg Beckert et al 2001) Its taxonomic status however stillremains to be clarified On the one hand most molecular studies resolve Takakiaand Sphagnum as sister genera although only partly with high statistical supportThese molecular topologies do not support the recognition of division Takakiophytaas proposed by Crandall-Stotler (1986) One the other hand no morphologicalsynapomorphies unite Takakia with Sphagnum and significant molecular differencesseparating Takakia from all other mosses were also observed For example a regionin the plastid ITS3 is similar to that of other land plants but absent in mosses(Samigullin et al 2002) and a transition in the trnL

UAA gene changing the anticodon

to CAA was otherwise only found in leptosporangiate ferns and Ginkgo (Quandt etal 2004) Thus ldquoresolution of Sphagnum - Takakia clade may be an artifactrdquo (Shawamp Renzaglia 2004) Also Goffinet amp Buck (2004) did not unite Takakia and Sphagnumunder a formal taxonomic rank but placed them into different informal superclassesIn our opinion Takakia should be treated at the same level as Sphagnophytina andBryophytina (cf Doweld 2001) ie as a subdivision of Bryophyta However morefundamental nomenclatural changes are necessary as the family name Takakiaceaewas not validated in the original publication by Hattori amp Inoue (1958) (article411 of ICBN McNeill et al 2006) and consequently all higher taxa erected laterare invalid The corrected taxonomic treatment of Takakia is provided here withsporophytic characters included in the latin diagnosis of Takakiaceae (see taxonomy)

Within Bryophytina we recognise four morphologically and molecularly isolatedbasal lineages as separated from the arthrodontous mosses (Bryopsida) Andreaeopsida(with linear capsule dehiscence) the operculate but eperistomate Oedipodiopsida aswell as Polytrichopsida and Tetraphidopsida with nematodontous peristomes A fifthclass Andreaeobryopsida was erected by Buck amp Goffinet (2000) but re-includedin Andreaeopsida as a subclass by Ochyra et al (2003) The systematic status of

8

Andreaeobryum macrosporum Steere amp BMMurray and possible relationships withAndreaea and Takakia were discussed by Murray (1988) and summarised includingmolecular results by Shaw amp Renzaglia (2004)

On the next lower level a number of morphologically and molecularly divergentlineages are nowadays treated as subclasses of Bryopsida Buxbaumiidae andDiphysciidae are generally branching off first in molecular topologies (eg Beckertet al 2001 Magombo 2003 Cox et al 2004) followed by Timmiidae Encalyptidaeand Funariidae as well as Dicranidae (haplolepideous mosses) sister to Bryidae slThese subclasses (except Buxbaumiidae not included) are also well recognizable inthe present analysis of non-coding plastid sequences (Fig 1)

The morphologically very different Encalyptidae and Funariidae are revealed assister groups although mostly without high support in several molecular phylogenies(eg Goffinet et al 2001 Cox et al 2004 Hedderson et al 2004 Tsubota et al2003 2004) and also in the present study (Fig 1) Goffinet et al (2007) confirmedthis relationship by phylogenomic evidence namely a large (71 kb) inversion in thechloroplast genome of Funariaceae Disceliaceae and Encalyptaceae but not inGigaspermaceae Consequently the latter family was separated at ordinal level fromthe two remaining families of Funariales by Goffinet et al (2007) GigaspermalesFunariales and Encalyptales may share a common ancestor according to some butnot all molecular phylogenies (eg Goffinet et al 2001 2007 Hedderson et al2004 but not in Tsubota et al 2004) Although ontogenetic data from peristomedevelopment may support their common ancestry (Goffinet et al 2007) unambiguousmorphological synapomorphies are lacking We therefore propose to treatGigaspermaceae at subclass level within the Bryopsida (see taxonomy)

The haplolepideous mosses (Dicranidae) are clearly supported as a monophyleticlineage which obviously evolved from a diplolepideous ancestor according to theirposition in the molecular trees (eg Newton et al 2000 Tsubota et al 2003 Cox etal 2004 Goffinet amp Buck 2004) Molecular studies suitable for inferring ordinaland family level relationships within Dicranidae either focused on the haplolepideousmosses (eg Stech 1999ab 2004 LaFarge et al 2000 2002 Tsubota et al 2003Hedderson et al 2004) or included more than 15 haplolepideous taxa in analyses ofa broader range of mosses (eg Goffinet et al 2001 Tsubota et al 2004 this study)Major lineages supported by these analyses are for example Grimmiales(Grimmiaceae Ptychomitriaceae and Seligeriaceae) Leucobryaceae (incl formerDicranaceae-Campylopoideae and Paraleucobryoideae pp) Dicranaceae sstr(Dicranoideae plus former Dicnemonaceae and Paraleucobryoideae pp) Pottiaceae(incl Cinclidotaceae and Splachnobryum) and Calymperaceae (probably exclOctoblepharum) Furthermore several genera and families belong to Dicranidaewhose systematic positions have been controversial (eg Stech et al 1999b LaFarge et al 2002 Hedderson et al 2004 OBrien 2007 Quandt et al 2007 thisstudy) Amphidium Archidium Catoscopium Drummondia EphemeraceaeErpodiaceae Mittenia (cf OBrien 2007 sequences in some earlier analyses werebased on misdentified specimens) Rhachitheciaceae Schistostega Splachnobryumand Wardia On the contrary several problems remain such as the circumscriptionof Ditrichaceae and relationships of the major haplolepideous lineages in general

9

Fig 1 Strict consensus tree of 129 most parsimonious trees inferred from combined trnLUAA

intronatpB-rbcL spacer and psbA-trnH spacer sequences of 85 taxa of Bryopsida as well as Andreaearupestris (Andreaeopsida) and Pogonatum subulatum (Polytrichopsida) as outgroup representativesBootstrap support values gt50 are depicted above the branches

10

Consequently resolving the phylogeny of Dicranidae with confidence is one of themajor future challenges in moss systematics

As mentioned above Dicranaceae are monophyletic in a narrow circumscriptionaccording to molecular data In contrast to former Campylopoideae andParaleucobryoideae the status of Rhabdoweisioideae (= Oncophoroideae Ochyra2002) and Dicranelloideae needs further consideration Stech (1999ab) suggestedto recognise RhabdoweisioideaeRhabdoweisiaceae in a broad sense includingDicranoweisia Amphidium and Aongstroemia Subsequent molecular analysesconfirmed a close relationship of the genera Arctoa Cynodontium DicranoweisiaKiaeria Oncophorus Oreoweisia Oreas Rhabdoweisia and Symblepharis althoughwithout significant support (La Farge et al 2002 Tsubota et al 2003 Hedderson etal 2004) With respect to the molecular evidence available so far we propose toelevate Oncophoroideae to family level to accomodate these genera and perhapsGlyphomitrium (cf Tsubota et al 2003) whereas we consider AongstroemiaDichodontium and Diobelonella to belong to Aongstroemiaceae (cf Stech 1999a)Amphidium is neither closely related to Dicranaceae sstr nor to Oncophoroideae(La Farge et al 2002 Tsubota et al 2003 Hedderson et al 2004 Stech 2004 thisstudy) and should be treated at family level rather than placed in Dicranaceae assubfam Amphidioideae (Ochyra et al 2003) The circumscription of Dicranelloideaeis more difficult to evaluate as few representatives have been included in molecularanalyses However Dicranella heteromalla (Hedw) Schimp as well as the generaCampylopodium and Microcampylopus are clearly separated from Dicranaceae sstr(Stech 1999a 2004 La Farge et al 2002 Tsubota et al 2003 Hedderson et al2004) and consequently the subfamily deserves family status as well Finallymolecular data showed that the genus Hypodontium does not belong to Pottiaceae(Hedderson et al 2004 Tsubota et al 2004) Taxonomic conclusions have not beendrawn from these results which is made up here (see taxonomy)

All mosses with diplolepideous-alternate peristomes together with Splachnales witha diplolepideous-opposite (Funaria-type) peristome form a monophyletic group inmolecular analyses (eg Newton et al 2000 Beckert et al 2001 Goffinet et al2001 Cox et al 2004 Tsubota et al 2004 references in Table 2) Differentclassifications of this by far most species-rich group of mosses were proposed (egVitt et al 1998 Ochyra et al 2003 Goffinet amp Buck 2004) However at least someof the recognised subclasses and superorders are paraphyletic according to themolecular topologies and assigning formal ranks to all evolutionarily significantmonophyletic entities is problematic if the main taxonomic framework of Bryophytaand Bryopsida should be maintained (cf discussion in Bell et al 2007) Thereforein the present synopsis only one subclass Bryidae is recognised for all diplolepideous-alternate mosses and Splachnales This broadly defined Bryidae is subdivided into13 orders most of them resolved as monophyletic in the majority of the phylogeneticanalyses summarised in Table 2 although with different levels of statistical supportin maximum parsimony analyses To define monophyletic lineages at supraordinallevel informal node-based names may be chosen according to Bell et al (2007) Forexample the pleurocarpous mosses (pleurocarpy sensu Bell amp Newton 2007) andtheir closest acrocarpous relatives (Orthodontiales to Hypnales) were already

11

Table 2 Taxon sampling and bootstrap support (BS) for Dicranidae Bryidae and orders within theBryidae in recent phylogenetic analyses (MP only) based on combined molecular markers Markersare given in square brackets (non-coding regions in bold) numbers of included taxa in brackets ++respective clade present with ge 80 BS + clade present with lt 80 BS - clade not present no oronly one representative included

Bell amp Newton OBrien Quandt et al Bell et al this study(2004) (2007) (2007) (2007)

[rbcL rps4 [atpB atpB- [rbcL rps4 [rbcL rps4 [atpB-rbcLnad5] rbcL rbcL trnL-F nad5] trnL-F nad5] psbA-trnH

rps4 trnL-F] trnL]

Dicranidae + (2) + (4) ++ (3) (1) ++ (19)Bryidae ++ (57) + (53) ++ (52) ++ (98) ++ (58)Hedwigiales ++ (2) (1) ++ (2) ++ (2) - (3)Bartramiales ++ (2) ++ (4) ++ (4) ++ (3) - (4)Splachnales (0) ++ (2) ++ (3) ++ (2) ++ (5)Bryales - (4) - (5) ++ (18) + (17) - (8)Orthotrichales (1) ++ (3) ++ (3) ++ (2) ++ (4)Orthodontiales + (4) + (4) + (3) + (6) - (3)Aulacomniales + (6) + (7) ++ (2) + (7) + (3)Rhizogoniales ++ (13) + (8) ++ (5) ++ (14) - (3)Hypnodendrales ++ (13) + (7) ++ (4) ++ (29) ++ (6)Ptychomniales ++ (3) ++ (3) (1) ++ (4) (1)Hookeriales - (4) + (2) (1) + (2) + (8)Hypnales - (5) - (7) ++ (5) ++ (10) + (10)

summarised under the informal node based name pleurcarpids (Bell et al 2007)and can be distinguished from a basal grade of acrocarpous or cladocarpous lineages(Hedwigiales to Orthotrichales) Within the latter monophyly of BartramialesSplachnales and Orthotrichales is well-supported in all analyses including two ormore taxa except Bartramiales in the present data set (cf Fig 1) In contrast Bryalesreceive significant support less frequently (but see Bell et al 2007 Quandt et al2007) Hedwigiales are well supported if only Hedwigia (Hedwigiaceae) andRhacocarpus (Rhacocarpaceae) are included whereas the monospecific Helicophyllum(Helicophyllaceae) is not closely related to these taxa but shows affinities withBartramiales (Goffinet et al 2001 this study) With respect to the differentmorphologies of Helicophyllaceae and Bartramiaceae however the former shouldbe separated at ordinal level (see taxonomy)

Clarifying relationships of the Orthotrichales is still a difficult issue Analyses ofsingle chloroplast markers or parsimony analyses of combined markers from differentgenomes mostly indicated a close relationship either with Splachnales (eg Cox etal 2000 Newton et al 2000 Tsubota et al 2004 Quandt et al 2007) or with thepleurocarpids (Goffinet et al 2001 this study) Although none of these alternativesis well-supported the latter seems more likely with regard to the moderately tomaximally supported Orthotrichales - pleurocarpid sister group relationship in allanalyses of mitochondrial data and in likelihood analyses of combined plastidmitochondrial markers (Beckert et al 2001 Quandt et al 2007)

12

The molecular polyphyly of Rhizogoniaceae (eg Bell amp Newton 2004) was solvedby the transfer of rhizogonioid genera into broadly defined Aulacomniaceae andOrthodontiaceae (Bell et al 2007) which now include both acrocarpous andpleurocarpous taxa These systematic changes are also comprehensible by non-molecular characters such as morphological traits shared by Mesochaete andAulacomnium heterostichum (Hedw) Bruch amp Schimp or the variously reducedperistomes of Orthodontiaceae pp in contrast to the generally fully developed Bryum-type peristomes of rhizogonioid and hypnodendroid mosses (Bell et al 2007) Theposition of the solely pleurocarpous Hypnodendrales sister to the former Hypnidaeled to the recognition of the informal group core pleurocarps (Bell et al 2007)The former Hypnidae (Ptychomniales Hookeriales and Hypnales summarised ashomocostate pleurocarps) are monophyletic in most molecular analyses (eg Goffinetet al 2001 Tsubota et al 2004 Bell et al 2007) with Ptychomniales being well-supported (Pedersen amp Newton 2007 Table 2) Clarifying relationships betweenHookeriales and Hypnales and within the latter is still a challenge but recent molecularstudies seem to support a sister group relationship of both orders (Bell et al 2007present study)

Phylogenetic utility of non-coding plastid markers

Non-coding plastid markers that comprise both variable and conserved regionssuch as the trnL

UAA intron have repeatedly been shown to possess potential for

resolving relationships at high taxonomic levels (eg Borsch et al 2003 Quandtet al 2004) Both the trnL intron and atpB-rbcL spacer were characterised indetail in mosses with respect to their structure and molecular evolution (Quandt ampStech 2005 Stech amp Quandt 2006) They include conservative regions that can beunambiguosly aligned and even parts of the more variable regions can be used ifrepeats hairpin loops etc are correctly identified and adequately treated in thephylogenetic analyses (eg Quandt et al 2003 Quandt amp Stech 2005) Using theatpB-rbcL spacer alone (Stech amp Quandt 2006) relationships of the major mosslineages were largely consistent with the ldquototal evidencerdquo molecular tree of Goffinetamp Buck (2004) However in addition to general limitations that result from singlemarker analyses the use of non-coding markers may pose further problems suchas a high amount of homoplasy resulting in low resolution or low statistical supportfor many clades Therefore several recent molecular studies of relationships withinBryidae have employed both coding and non-coding markers (Table 2)Nevertheless the usefulness of analyses of combined non-coding plastid markerscannot be ruled out In fact Fig 1 and Table 2 indicate a phylogenetic signal inthe present data set as many clades are recovered that are usually also resolvedin analyses of coding or combined coding and non-coding markers Especiallywith regard to statistical support however the present analysis is inferior tothose of other recent data sets especially Bell et al (2007) and Quandt et al(2007) In addition the non-coding markers used here are of different suitabilityand even the two intergenic spacers differ considerably from each other ThepsbA-trnH spacer contributes much less to the trees resolution than the atpB-rbcL spacer first because it is much shorter and second because relatively largeparts are attributed to hairpin loops or otherwise hypervariable regions These

13

results indicate that future studies should evaluate the molecular evolution andphylogenetic potential of new markers both coding and con-coding and choosethe most suitable ones in a combined analysis to resolve the remaining uncertaintiesin moss phylogeny

Taxonomy

Takakiaceae Stech amp WFrey stat nov

Plantae virides nusquam rhizophorae sine protonemate e caudicis rhizomatis erectae Caudicesrhizomati et axes geotropi radiformes frequenter intercalariter ramificantes sine phyllidiis cumpapillis mucilaginis rostratis Caules phyllidiiferi saepe furcati Phyllidia sine lamina et costadistincta profunde 2-4(-5)-lobata pluristratosa tristicha sed torsione spiraliter disposita Filumcentralium in ambabus generationibus (axibus gametophyti et setis) adest Plantae dioicae Antheridiaet archegonia nuda Sporophytum terminale solitarium Seta persistens Capsula tortilis admaturitatem schizocarpa secus unam rimam spiralem longitudinalem dehiscens Stomata etoperculum absunt peristomium nullum Calyptra mitriformis

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiaceae SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval (Art 411)

Takakiales Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiales SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval

Takakiales SHatt amp Inoue ex RMSchust J Hattori Bot Lab 26 224 1963 nom inval (cumdescr latin)

Takakiopsida Stech amp WFrey statnov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiopsida Goffinet amp WRBuck Monogr Syst Bot Missouri Bot Gard 98 232 2004 nominval

Takakiopsida Jia et al Acta Phytotax Sin 41 350 351 2003 nom nud

Takakiopsida Wang amp Wu Fl Bryophyt Sin 8 447 2004 nom inval (cum descr latin)

Takakiophytina Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue JHattori Bot Lab 19 137 1958

Gigaspermidae Stech amp WFrey subclass nov

Plantae acrocarpae terrestres stoloniferae ramis brevibus erectis Folia unicostata cellulis laxislaevibus Capsula plerumque valde rugosa gymnostomatica vel cleistocarpa stomata cum duabuscellulis sociis Ab Funariidis et Encalyptidis charactere phylogenomico (71-kb inversio abest)separatae

14

TYPUS Gigaspermum Lindb Oumlfversigt af Foumlrhandlingar Kongl Svenska Vetenskaps-Akademien21 599 1865

Amphidiaceae Stech stat nov

Based on Dicranaceae subfam Amphidioideae Ochyra in Ochyra Zarnowiec amp Bednarek-OchyraCens Cat Polish Mosses 110 2003

TYPUS Amphidium Schimp Coroll Bryol Eur 39 1856

Amphidiaceae AJESm Moss Fl Britain Ireland 2nd ed 657 2004 nom inval descr angl

Dicranellaceae Stech stat nov

Based on Dicranaceae subfam Dicranelloideae Lindb Utkast Eur Bladmoss 33 1878[lsquoUnderfamilje Dicranelleaersquo]

TYPUS Dicranella (MuumlllHal) Schimp Coroll Bryol Eur 13 1856

Oncophoraceae Stech stat nov

Based on Dicranaceae subfam Oncophoroideae Lindb Utkast Eur Bladmoss 34 1878[lsquoUnderfamilje Oncophoreaersquo]

TYPUS Oncophorus (Brid) Brid Bryol Univ 1 389 1826

Hypodontiaceae Stech fam nov

Plantae robustae characteribus morphologicis Pottiaceis et Calymperaceis similes sedcharacteribus molecularicis separatae Bracteae perichaetiales internae e basi vaginantes subulataevel aristatae Capsula aspectu succulenta cellulae exothecii incrassatae annulus magnopereabsens Peristomii dentes breves triangulati incurvati aurantiaci leves vel infirme verrucosiCalyptra cucullata

TYPUS Hypodontium MuumlllHal Hedwigia 38 96 1899

Helicophyllales Stech amp WFrey ord nov

Plantae acrocarpae prostratae tomentosae Folia dimorpha in duas series laterales et unam seriemventralem divisa Costa percurrens Cellulae hexagonae ad subquadratae papillosae Capsula immersacupulata ad oblonga infra orificium abrupte incurvata stomata destituta Peristomium nullum Sporaeisomorphae heteropolares granulatae

TYPUS Helicophyllum Brid Bryol Univ 2 771 1827

Synopsis of the suprageneric classification of BryophytaAuthor citations are in accordance with Art 492 of the Vienna Code (McNeill et al 2006)

Subdivision Takakiophytina Stech amp WFreyClass Takakiopsida Stech amp WFrey

Order Takakiales Stech amp WFreyTakakiaceae Stech amp WFrey

Subdivision Sphagnophytina DoweldClass Sphagnopsida Schimp

Order Sphagnales Limpr

15

Sphagnaceae DumortOrder Ambuchananiales Seppelt amp HACrum

Ambuchananiaceae Seppelt amp HACrumSubdivision Bryophytina Engler

Class Andreaeopsida JHSchaffnSubclass Andreaeidae Engl

Order Andreaeales LimprAndreaeaceae Dumort

Subclass Andreaeobryidae OchyraOrder Andreaeobryales BMMurray

Andreaeobryaceae Steere amp BMMurrayClass Oedipodiopsida Goffinet amp WRBuck

Order Oedipodiales Goffinet amp WRBuckOedipodiaceae Schimp

Class Tetraphidopsida Goffinet amp WRBuckOrder Tetraphidales MFleisch

Tetraphidaceae SchimpClass Polytrichopsida Doweld

Order Polytrichales MFleischPolytrichaceae Schwaumlgr

Class Bryopsida PaxSubclass Buxbaumiidae Doweld

Order Buxbaumiales MFleischBuxbaumiaceae Schimp

Subclass Diphysciidae OchyraOrder Diphysciales MFleisch

Diphysciaceae MFleischSubclass Timmiidae Ochyra

Order Timmiales OchyraTimmiaceae Schimp

Subclass Encalyptidae Ochyra Żarnowiec amp Bednarek-OchyraOrder Encalyptales Dixon

Encalyptaceae SchimpSubclass Funariidae Ochyra

Order Funariales MFleischFunariaceae Schwaumlgr Disceliaceae Schimp

Subclass Gigaspermidae Stech amp WFreyOrder Gigaspermales Goffinet Wickett OWerner Ros AJShaw amp CJCox

Gigaspermaceae LindbSubclass Dicranidae Doweld

Order Catoscopiales Ignatov amp IgnatovaCatoscopiaceae Broth

Order Scouleriales Goffinet amp WRBuckDrummondiaceae Goffinet Scouleriaceae SPChurchill

Order Bryoxiphiales HACrum amp LEAndersonBryoxiphiaceae Besch

16

Order Grimmiales MFleischGrimmiaceae Arn Ptychomitriaceae Schimp Seligeriaceae Schimp

Order Archidiales LimprArchidiaceae Schimp

Order Mitteniales ShawMitteniaceae Broth

Order Dicranales HPhilib ex MFleischAmphidiaceae Stech Aongstroemiaceae De Not BruchiaceaeSchimp Calymperaceae Kindb Dicranaceae Schimp Dicranel-laceae Stech Ditrichaceae Limpr Erpodiaceae Broth EustichiaceaeBroth Fissidentaceae Schimp Leucobryaceae Schimp Onco-phoraceae Stech Rhachitheciaceae HRob Schistostegaceae SchimpViridivelleraceae IGStone Wardiaceae Welch

Order Pottiales MFleischEphemeraceae Schimp Hypodontiaceae Stech PleurophascaceaeBroth Pottiaceae Schimp Serpotortellaceae WDReese amp RHZander

Subclass Bryidae EnglOrder Hedwigiales Ochyra

Hedwigiaceae Schimp Rhacocarpaceae KindbOrder Helicophyllales Stech amp WFrey

Helicophyllaceae BrothOrder Bartramiales DQuandt NEBell amp Stech

Bartramiaceae SchwaumlgrOrder Splachnales Ochyra

Meesiaceae Schimp Splachnaceae Grev amp ArnOrder Bryales Limpr

Bryaceae Schwaumlgr Leptostomataceae Schwaumlgr Mniaceae SchwaumlgrPhyllodrepaniaceae Crosby Pseudoditrichaceae Steere amp ZIwatsPulchrinodaceae DQuandt NEBell amp Stech

Order Orthotrichales DixonOrthotrichaceae Arn

Order Orthodontiales NEBell AENewton amp DQuandtOrthodontiaceae Goffinet

Order Aulacomniales NEBell AENewton amp DQuandtAulacomniaceae Schimp

Order Rhizogoniales Goffinet amp WRBuckRhizogoniaceae Broth

Order Hypnodendrales NEBell AENewton amp DQuandtBraithwaiteaceae NEBell AENewton amp DQuandt Hypnodendra-ceae Broth Pterobryellaceae WRBuck amp Vitt Racopilaceae Kindb

Order Ptychomniales WRBuck CJCox AJShaw amp GoffinetPtychomniaceae MFleisch

Order Hookeriales MFleischDaltoniaceae Schimp Hookeriaceae Schimp HypopterygiaceaeMitt Leucomiaceae Broth Pilotrichaceae Kindb SaulomataceaeWRBuck CJCox AJShaw amp Goffinet Schimperobryaceae WR

17

Buck CJCox AJShaw amp GoffinetOrder Hypnales WRBuck amp Vitt

Amblystegiaceae GRoth Anomodontaceae Kindb BrachytheciaceaeSchimp Calliergonaceae Vanderpoorten Hedenaumls CJCox amp AJShaw Catagoniaceae WRBuck amp Ireland Climaciaceae KindbCryphaeaceae Schimp Echinodiaceae Broth Entodontaceae KindbFabroniaceae Schimp Fontinalaceae Schimp Helodiaceae OchyraHeterocladiaceae Ignatov amp Ignatova Hylocomiaceae MFleischHypnaceae Schimp Lembophyllaceae Broth LeptodontaceaeSchimp Lepyrodontaceae Broth Leskeaceae Schimp Leucodon-taceae Schimp Meteoriaceae Kindb Microtheciellaceae HAMillamp AJHarr Myriniaceae Schimp Myuriaceae MFleisch NeckeraceaeSchimp Orthorrhynchiaceae SHLin Phyllogoniaceae KindbPlagiotheciaceae MFleisch Pleuroziopsidaceae Ireland Prionodon-taceae Broth Pseudoleskeaceae Schimp PseudoleskeellaceaeIgnatov amp Ignatova Pterigynandraceae Schimp PterobryaceaeKindb Pylaisiaceae Schimp Pylaisiadelphaceae Goffinet amp WRBuck Regmatodontaceae Broth Rhytidiaceae Broth RigodiaceaeHACrum Rutenbergiaceae MFleisch Scorpidiaceae Ignatov ampIgnatova Sematophyllaceae Broth Sorapillaceae MFleisch Ste-reophyllaceae WRBuck amp Ireland Symphyodontaceae MFleischTheliaceae MFleisch Thuidiaceae Schimp TrachylomataceaeWRBuck amp Vitt

Acknowledgements

Sincere thanks are due to JLReveal (Ithaca) as well as WFPrudhomme van Reine and JFVeldkamp(Leiden) for comments and discussions about suprafamilial taxonomy to DQuandt (Dresden) for providingDNA from Rhacocarpus and Bartramiaceae species and to BGiesicke (Berlin) for technical assistance

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18

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19

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21

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TSUBOTA H Y AGENO B ESTEacuteBANEZ T YAMAGUCHI amp H DEGUCHI (2003)Molecular phylogeny of the Grimmiales (Musci) based on chloroplast rbcL sequences - Hikobia 1455-70

TSUBOTA H E DE LUNA D GONZAacuteLEZ MS IGNATOV amp H DEGUCHI (2004) Molecularphylogenetics and ordinal relationships based on analyses of a large-scale data set of 600 rbcLsequences of mosses - Hikobia 14 149-170

VITT DH (1984) Classification of the Bryopsida - In SCHUSTER RM (ed) New Manual ofBryology 2 696-759 Hattori Botanical Laboratory Nichinan Japan

VITT DH B GOFFINET amp T HEDDERSON (1998) 8 The ordinal classification of the mossesquestions and answers for the 1990s - In BATES JW NW ASHTON amp JG DUCKETT (eds)Bryology for the twenty-first century British Bryol Soc pp 113-123

Received 3 September 2007 accepted in revised form 30 October 2007

Page 6: botanica parcial 3

6

primers CM

DM

(slightly modified after Taberlet et al 1991 see Frey et al 1999) and atpB-1rbcL-1(Chiang et al 1998) respectively For amplification of the psbA-trnH spacer primers psbAF(5-GTT ATG CAT GAA CGT AAT GCT C-3 Sang et al 1997) and trnHR-2 (5-CGC GCA TGGTGG ATT CAC AAT CC-3 slightly modified after Sang et al 1997) were used with a PCRprotocol of 5 min 94degC 35 cycles (30 sec 94degC 1 min 48degC 1 min 40 sec 72degC) 7 min 72degC PCRproducts were purified using DNA purification kits (Qiagen Macherey-Nagel) Sequencing wasperformed as described in Stech (2004) using the amplification primers

ALIGNMENT AND PHYLOGENETIC ANALYSES DNA sequences were manually aligned in PhyDE v0992(Muumlller et al 2005) Following Quandt et al (2003) and Quandt amp Stech (2005) inversions inputative hairpin secondary structures were positionally separated in the alignment their presence orabsence was not coded for the phylogenetic analyses Phylogenetic reconstructions under the maximumparsimony criterion were performed using winPAUP 40b10 (Swofford 2002) in combination withPRAP (Muumlller 2004) as implemented in SeqState (Muumlller 2005) PRAP generates command filesfor PAUP that allow parsimony ratchet searches as designed by Nixon (1999) Heuristic searchesunder parsimony were performed with the following options all characters equally weighted andunordered TBR branch swapping collapse branches if maximum branch length is zero MulTreesoption in effect gaps treated as missing data Initially a heuristic search with 1000 addition sequencereplicates was performed For the parsimony ratchet ten random addition cycles of 200 ratchetiterations each were used with TBR branch swapping on a randomly re-weighted data set (25 ofthe positions) Heuristic bootstrap searches were performed with 1000 replicates with 10 additionsequence replicates per bootstrap replicate

Results

In the present data set of non-coding plastid markers sequence lengths ranged from243 to 368 nucleotides (nt) in the trnL intron and from 445 to 615 nt in the atpB-rbcL spacer The psbA-trnH spacer was considerably shorter than the other twomarkers and ranged from 103 to 186 nt The combined alignment of sequences from85 ingroup and two outgroup taxa comprised 2430 positions (trnL intron 668 atpB-rbcL spacer 1366 psbA-trnH spacer 396 positions) The most variable regions withambiguous alignment (781 positions) were excluded from phylogenetic analysis Ofthe 1649 included positions 628 (381) were variable and 455 of the variablepositions (725 or 276 of the total number of positions) were parsimony-informative The trnL intron comprised 124 the atpB-rbcL spacer 286 and the psbA-trnH spacer 45 of these included parsimony-informative positions

The shortest trees found in the heuristic maximum parsimony analysis of the combineddata set had a length of 2433 steps By applying the parsimony ratchet 129 treeswere retained that were one step shorter (length 2432 CI = 0419 RI = 0624) Thestrict consensus tree of the ratchet analysis is shown in Fig 1 The ingroup (Bryopsida)is supported with 100 bootstrap support (BS) Diphysciidae are sister to theremaining Bryopsida with 54 BS Encalyptidae Funariidae Timmiidae andDicranidae all receive gt 95 BS while Bryidae are slightly less supported (89BS) Relationships between these major lineages are resolved but unsupported Atordinal level within the Bryidae a lower resolution is observed SplachnalesOrthotrichales Aulacomniales Hypnodendrales Hookeriales and Hypnales areresolved as monophyletic with 67-100 BS whereas Hedwigiales BartramialesBryales Orthodontiales and Rhizogoniales are not A closer relationship ofOrthotrichales with the pleurocarpous mosses sl than with the more basal ordersHedwigiales Bartramiales Splachnales and Bryales is indicated

7

Discussion

Classification of mosses - recent progress and the current state

For a long time mosses were subdivided into three main lineages the subclassesSphagnidae Andreaeidae and Bryidae (eg Fleischer 1920 Vitt 1984 Frahm ampFrey 1987) the latter with a number of (super-)orders (eg Frey 1977) Howevermolecular data confirmed that mosses comprise a number of isolated basal lineagesrepresented by morphologically and ecologically distinct extant taxa such as TakakiaSphagnum Andreaea Andreaeobryum Oedipodium Tetraphis the Polytrichaceaeand Buxbaumia which probably have long independent phylogenetic histories (cfNewton et al 2007) As a result of molecular phylogenies and a re-evaluation ofmorphological-anatomical characters the classification of mosses has changedconsiderably in the last few years with the main lineages nowadays treated atsubdivision class and subclass levels within division Bryophyta (eg Doweld 2001Ochyra et al 2003 Goffinet amp Buck 2004 this study)

Takakia and Sphagnum are the earliest diverging moss taxa in molecular phylogenies(eg Newton et al 2000 Beckert et al 2001 Cox et al 2004 Qiu et al 2006Newton et al 2007) That Takakia is a moss and not a liverwort was confirmed byanalysis of DNA sequences and phylogenomic characters such as the distribution ofmitochondrial introns (eg Beckert et al 2001) Its taxonomic status however stillremains to be clarified On the one hand most molecular studies resolve Takakiaand Sphagnum as sister genera although only partly with high statistical supportThese molecular topologies do not support the recognition of division Takakiophytaas proposed by Crandall-Stotler (1986) One the other hand no morphologicalsynapomorphies unite Takakia with Sphagnum and significant molecular differencesseparating Takakia from all other mosses were also observed For example a regionin the plastid ITS3 is similar to that of other land plants but absent in mosses(Samigullin et al 2002) and a transition in the trnL

UAA gene changing the anticodon

to CAA was otherwise only found in leptosporangiate ferns and Ginkgo (Quandt etal 2004) Thus ldquoresolution of Sphagnum - Takakia clade may be an artifactrdquo (Shawamp Renzaglia 2004) Also Goffinet amp Buck (2004) did not unite Takakia and Sphagnumunder a formal taxonomic rank but placed them into different informal superclassesIn our opinion Takakia should be treated at the same level as Sphagnophytina andBryophytina (cf Doweld 2001) ie as a subdivision of Bryophyta However morefundamental nomenclatural changes are necessary as the family name Takakiaceaewas not validated in the original publication by Hattori amp Inoue (1958) (article411 of ICBN McNeill et al 2006) and consequently all higher taxa erected laterare invalid The corrected taxonomic treatment of Takakia is provided here withsporophytic characters included in the latin diagnosis of Takakiaceae (see taxonomy)

Within Bryophytina we recognise four morphologically and molecularly isolatedbasal lineages as separated from the arthrodontous mosses (Bryopsida) Andreaeopsida(with linear capsule dehiscence) the operculate but eperistomate Oedipodiopsida aswell as Polytrichopsida and Tetraphidopsida with nematodontous peristomes A fifthclass Andreaeobryopsida was erected by Buck amp Goffinet (2000) but re-includedin Andreaeopsida as a subclass by Ochyra et al (2003) The systematic status of

8

Andreaeobryum macrosporum Steere amp BMMurray and possible relationships withAndreaea and Takakia were discussed by Murray (1988) and summarised includingmolecular results by Shaw amp Renzaglia (2004)

On the next lower level a number of morphologically and molecularly divergentlineages are nowadays treated as subclasses of Bryopsida Buxbaumiidae andDiphysciidae are generally branching off first in molecular topologies (eg Beckertet al 2001 Magombo 2003 Cox et al 2004) followed by Timmiidae Encalyptidaeand Funariidae as well as Dicranidae (haplolepideous mosses) sister to Bryidae slThese subclasses (except Buxbaumiidae not included) are also well recognizable inthe present analysis of non-coding plastid sequences (Fig 1)

The morphologically very different Encalyptidae and Funariidae are revealed assister groups although mostly without high support in several molecular phylogenies(eg Goffinet et al 2001 Cox et al 2004 Hedderson et al 2004 Tsubota et al2003 2004) and also in the present study (Fig 1) Goffinet et al (2007) confirmedthis relationship by phylogenomic evidence namely a large (71 kb) inversion in thechloroplast genome of Funariaceae Disceliaceae and Encalyptaceae but not inGigaspermaceae Consequently the latter family was separated at ordinal level fromthe two remaining families of Funariales by Goffinet et al (2007) GigaspermalesFunariales and Encalyptales may share a common ancestor according to some butnot all molecular phylogenies (eg Goffinet et al 2001 2007 Hedderson et al2004 but not in Tsubota et al 2004) Although ontogenetic data from peristomedevelopment may support their common ancestry (Goffinet et al 2007) unambiguousmorphological synapomorphies are lacking We therefore propose to treatGigaspermaceae at subclass level within the Bryopsida (see taxonomy)

The haplolepideous mosses (Dicranidae) are clearly supported as a monophyleticlineage which obviously evolved from a diplolepideous ancestor according to theirposition in the molecular trees (eg Newton et al 2000 Tsubota et al 2003 Cox etal 2004 Goffinet amp Buck 2004) Molecular studies suitable for inferring ordinaland family level relationships within Dicranidae either focused on the haplolepideousmosses (eg Stech 1999ab 2004 LaFarge et al 2000 2002 Tsubota et al 2003Hedderson et al 2004) or included more than 15 haplolepideous taxa in analyses ofa broader range of mosses (eg Goffinet et al 2001 Tsubota et al 2004 this study)Major lineages supported by these analyses are for example Grimmiales(Grimmiaceae Ptychomitriaceae and Seligeriaceae) Leucobryaceae (incl formerDicranaceae-Campylopoideae and Paraleucobryoideae pp) Dicranaceae sstr(Dicranoideae plus former Dicnemonaceae and Paraleucobryoideae pp) Pottiaceae(incl Cinclidotaceae and Splachnobryum) and Calymperaceae (probably exclOctoblepharum) Furthermore several genera and families belong to Dicranidaewhose systematic positions have been controversial (eg Stech et al 1999b LaFarge et al 2002 Hedderson et al 2004 OBrien 2007 Quandt et al 2007 thisstudy) Amphidium Archidium Catoscopium Drummondia EphemeraceaeErpodiaceae Mittenia (cf OBrien 2007 sequences in some earlier analyses werebased on misdentified specimens) Rhachitheciaceae Schistostega Splachnobryumand Wardia On the contrary several problems remain such as the circumscriptionof Ditrichaceae and relationships of the major haplolepideous lineages in general

9

Fig 1 Strict consensus tree of 129 most parsimonious trees inferred from combined trnLUAA

intronatpB-rbcL spacer and psbA-trnH spacer sequences of 85 taxa of Bryopsida as well as Andreaearupestris (Andreaeopsida) and Pogonatum subulatum (Polytrichopsida) as outgroup representativesBootstrap support values gt50 are depicted above the branches

10

Consequently resolving the phylogeny of Dicranidae with confidence is one of themajor future challenges in moss systematics

As mentioned above Dicranaceae are monophyletic in a narrow circumscriptionaccording to molecular data In contrast to former Campylopoideae andParaleucobryoideae the status of Rhabdoweisioideae (= Oncophoroideae Ochyra2002) and Dicranelloideae needs further consideration Stech (1999ab) suggestedto recognise RhabdoweisioideaeRhabdoweisiaceae in a broad sense includingDicranoweisia Amphidium and Aongstroemia Subsequent molecular analysesconfirmed a close relationship of the genera Arctoa Cynodontium DicranoweisiaKiaeria Oncophorus Oreoweisia Oreas Rhabdoweisia and Symblepharis althoughwithout significant support (La Farge et al 2002 Tsubota et al 2003 Hedderson etal 2004) With respect to the molecular evidence available so far we propose toelevate Oncophoroideae to family level to accomodate these genera and perhapsGlyphomitrium (cf Tsubota et al 2003) whereas we consider AongstroemiaDichodontium and Diobelonella to belong to Aongstroemiaceae (cf Stech 1999a)Amphidium is neither closely related to Dicranaceae sstr nor to Oncophoroideae(La Farge et al 2002 Tsubota et al 2003 Hedderson et al 2004 Stech 2004 thisstudy) and should be treated at family level rather than placed in Dicranaceae assubfam Amphidioideae (Ochyra et al 2003) The circumscription of Dicranelloideaeis more difficult to evaluate as few representatives have been included in molecularanalyses However Dicranella heteromalla (Hedw) Schimp as well as the generaCampylopodium and Microcampylopus are clearly separated from Dicranaceae sstr(Stech 1999a 2004 La Farge et al 2002 Tsubota et al 2003 Hedderson et al2004) and consequently the subfamily deserves family status as well Finallymolecular data showed that the genus Hypodontium does not belong to Pottiaceae(Hedderson et al 2004 Tsubota et al 2004) Taxonomic conclusions have not beendrawn from these results which is made up here (see taxonomy)

All mosses with diplolepideous-alternate peristomes together with Splachnales witha diplolepideous-opposite (Funaria-type) peristome form a monophyletic group inmolecular analyses (eg Newton et al 2000 Beckert et al 2001 Goffinet et al2001 Cox et al 2004 Tsubota et al 2004 references in Table 2) Differentclassifications of this by far most species-rich group of mosses were proposed (egVitt et al 1998 Ochyra et al 2003 Goffinet amp Buck 2004) However at least someof the recognised subclasses and superorders are paraphyletic according to themolecular topologies and assigning formal ranks to all evolutionarily significantmonophyletic entities is problematic if the main taxonomic framework of Bryophytaand Bryopsida should be maintained (cf discussion in Bell et al 2007) Thereforein the present synopsis only one subclass Bryidae is recognised for all diplolepideous-alternate mosses and Splachnales This broadly defined Bryidae is subdivided into13 orders most of them resolved as monophyletic in the majority of the phylogeneticanalyses summarised in Table 2 although with different levels of statistical supportin maximum parsimony analyses To define monophyletic lineages at supraordinallevel informal node-based names may be chosen according to Bell et al (2007) Forexample the pleurocarpous mosses (pleurocarpy sensu Bell amp Newton 2007) andtheir closest acrocarpous relatives (Orthodontiales to Hypnales) were already

11

Table 2 Taxon sampling and bootstrap support (BS) for Dicranidae Bryidae and orders within theBryidae in recent phylogenetic analyses (MP only) based on combined molecular markers Markersare given in square brackets (non-coding regions in bold) numbers of included taxa in brackets ++respective clade present with ge 80 BS + clade present with lt 80 BS - clade not present no oronly one representative included

Bell amp Newton OBrien Quandt et al Bell et al this study(2004) (2007) (2007) (2007)

[rbcL rps4 [atpB atpB- [rbcL rps4 [rbcL rps4 [atpB-rbcLnad5] rbcL rbcL trnL-F nad5] trnL-F nad5] psbA-trnH

rps4 trnL-F] trnL]

Dicranidae + (2) + (4) ++ (3) (1) ++ (19)Bryidae ++ (57) + (53) ++ (52) ++ (98) ++ (58)Hedwigiales ++ (2) (1) ++ (2) ++ (2) - (3)Bartramiales ++ (2) ++ (4) ++ (4) ++ (3) - (4)Splachnales (0) ++ (2) ++ (3) ++ (2) ++ (5)Bryales - (4) - (5) ++ (18) + (17) - (8)Orthotrichales (1) ++ (3) ++ (3) ++ (2) ++ (4)Orthodontiales + (4) + (4) + (3) + (6) - (3)Aulacomniales + (6) + (7) ++ (2) + (7) + (3)Rhizogoniales ++ (13) + (8) ++ (5) ++ (14) - (3)Hypnodendrales ++ (13) + (7) ++ (4) ++ (29) ++ (6)Ptychomniales ++ (3) ++ (3) (1) ++ (4) (1)Hookeriales - (4) + (2) (1) + (2) + (8)Hypnales - (5) - (7) ++ (5) ++ (10) + (10)

summarised under the informal node based name pleurcarpids (Bell et al 2007)and can be distinguished from a basal grade of acrocarpous or cladocarpous lineages(Hedwigiales to Orthotrichales) Within the latter monophyly of BartramialesSplachnales and Orthotrichales is well-supported in all analyses including two ormore taxa except Bartramiales in the present data set (cf Fig 1) In contrast Bryalesreceive significant support less frequently (but see Bell et al 2007 Quandt et al2007) Hedwigiales are well supported if only Hedwigia (Hedwigiaceae) andRhacocarpus (Rhacocarpaceae) are included whereas the monospecific Helicophyllum(Helicophyllaceae) is not closely related to these taxa but shows affinities withBartramiales (Goffinet et al 2001 this study) With respect to the differentmorphologies of Helicophyllaceae and Bartramiaceae however the former shouldbe separated at ordinal level (see taxonomy)

Clarifying relationships of the Orthotrichales is still a difficult issue Analyses ofsingle chloroplast markers or parsimony analyses of combined markers from differentgenomes mostly indicated a close relationship either with Splachnales (eg Cox etal 2000 Newton et al 2000 Tsubota et al 2004 Quandt et al 2007) or with thepleurocarpids (Goffinet et al 2001 this study) Although none of these alternativesis well-supported the latter seems more likely with regard to the moderately tomaximally supported Orthotrichales - pleurocarpid sister group relationship in allanalyses of mitochondrial data and in likelihood analyses of combined plastidmitochondrial markers (Beckert et al 2001 Quandt et al 2007)

12

The molecular polyphyly of Rhizogoniaceae (eg Bell amp Newton 2004) was solvedby the transfer of rhizogonioid genera into broadly defined Aulacomniaceae andOrthodontiaceae (Bell et al 2007) which now include both acrocarpous andpleurocarpous taxa These systematic changes are also comprehensible by non-molecular characters such as morphological traits shared by Mesochaete andAulacomnium heterostichum (Hedw) Bruch amp Schimp or the variously reducedperistomes of Orthodontiaceae pp in contrast to the generally fully developed Bryum-type peristomes of rhizogonioid and hypnodendroid mosses (Bell et al 2007) Theposition of the solely pleurocarpous Hypnodendrales sister to the former Hypnidaeled to the recognition of the informal group core pleurocarps (Bell et al 2007)The former Hypnidae (Ptychomniales Hookeriales and Hypnales summarised ashomocostate pleurocarps) are monophyletic in most molecular analyses (eg Goffinetet al 2001 Tsubota et al 2004 Bell et al 2007) with Ptychomniales being well-supported (Pedersen amp Newton 2007 Table 2) Clarifying relationships betweenHookeriales and Hypnales and within the latter is still a challenge but recent molecularstudies seem to support a sister group relationship of both orders (Bell et al 2007present study)

Phylogenetic utility of non-coding plastid markers

Non-coding plastid markers that comprise both variable and conserved regionssuch as the trnL

UAA intron have repeatedly been shown to possess potential for

resolving relationships at high taxonomic levels (eg Borsch et al 2003 Quandtet al 2004) Both the trnL intron and atpB-rbcL spacer were characterised indetail in mosses with respect to their structure and molecular evolution (Quandt ampStech 2005 Stech amp Quandt 2006) They include conservative regions that can beunambiguosly aligned and even parts of the more variable regions can be used ifrepeats hairpin loops etc are correctly identified and adequately treated in thephylogenetic analyses (eg Quandt et al 2003 Quandt amp Stech 2005) Using theatpB-rbcL spacer alone (Stech amp Quandt 2006) relationships of the major mosslineages were largely consistent with the ldquototal evidencerdquo molecular tree of Goffinetamp Buck (2004) However in addition to general limitations that result from singlemarker analyses the use of non-coding markers may pose further problems suchas a high amount of homoplasy resulting in low resolution or low statistical supportfor many clades Therefore several recent molecular studies of relationships withinBryidae have employed both coding and non-coding markers (Table 2)Nevertheless the usefulness of analyses of combined non-coding plastid markerscannot be ruled out In fact Fig 1 and Table 2 indicate a phylogenetic signal inthe present data set as many clades are recovered that are usually also resolvedin analyses of coding or combined coding and non-coding markers Especiallywith regard to statistical support however the present analysis is inferior tothose of other recent data sets especially Bell et al (2007) and Quandt et al(2007) In addition the non-coding markers used here are of different suitabilityand even the two intergenic spacers differ considerably from each other ThepsbA-trnH spacer contributes much less to the trees resolution than the atpB-rbcL spacer first because it is much shorter and second because relatively largeparts are attributed to hairpin loops or otherwise hypervariable regions These

13

results indicate that future studies should evaluate the molecular evolution andphylogenetic potential of new markers both coding and con-coding and choosethe most suitable ones in a combined analysis to resolve the remaining uncertaintiesin moss phylogeny

Taxonomy

Takakiaceae Stech amp WFrey stat nov

Plantae virides nusquam rhizophorae sine protonemate e caudicis rhizomatis erectae Caudicesrhizomati et axes geotropi radiformes frequenter intercalariter ramificantes sine phyllidiis cumpapillis mucilaginis rostratis Caules phyllidiiferi saepe furcati Phyllidia sine lamina et costadistincta profunde 2-4(-5)-lobata pluristratosa tristicha sed torsione spiraliter disposita Filumcentralium in ambabus generationibus (axibus gametophyti et setis) adest Plantae dioicae Antheridiaet archegonia nuda Sporophytum terminale solitarium Seta persistens Capsula tortilis admaturitatem schizocarpa secus unam rimam spiralem longitudinalem dehiscens Stomata etoperculum absunt peristomium nullum Calyptra mitriformis

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiaceae SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval (Art 411)

Takakiales Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiales SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval

Takakiales SHatt amp Inoue ex RMSchust J Hattori Bot Lab 26 224 1963 nom inval (cumdescr latin)

Takakiopsida Stech amp WFrey statnov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiopsida Goffinet amp WRBuck Monogr Syst Bot Missouri Bot Gard 98 232 2004 nominval

Takakiopsida Jia et al Acta Phytotax Sin 41 350 351 2003 nom nud

Takakiopsida Wang amp Wu Fl Bryophyt Sin 8 447 2004 nom inval (cum descr latin)

Takakiophytina Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue JHattori Bot Lab 19 137 1958

Gigaspermidae Stech amp WFrey subclass nov

Plantae acrocarpae terrestres stoloniferae ramis brevibus erectis Folia unicostata cellulis laxislaevibus Capsula plerumque valde rugosa gymnostomatica vel cleistocarpa stomata cum duabuscellulis sociis Ab Funariidis et Encalyptidis charactere phylogenomico (71-kb inversio abest)separatae

14

TYPUS Gigaspermum Lindb Oumlfversigt af Foumlrhandlingar Kongl Svenska Vetenskaps-Akademien21 599 1865

Amphidiaceae Stech stat nov

Based on Dicranaceae subfam Amphidioideae Ochyra in Ochyra Zarnowiec amp Bednarek-OchyraCens Cat Polish Mosses 110 2003

TYPUS Amphidium Schimp Coroll Bryol Eur 39 1856

Amphidiaceae AJESm Moss Fl Britain Ireland 2nd ed 657 2004 nom inval descr angl

Dicranellaceae Stech stat nov

Based on Dicranaceae subfam Dicranelloideae Lindb Utkast Eur Bladmoss 33 1878[lsquoUnderfamilje Dicranelleaersquo]

TYPUS Dicranella (MuumlllHal) Schimp Coroll Bryol Eur 13 1856

Oncophoraceae Stech stat nov

Based on Dicranaceae subfam Oncophoroideae Lindb Utkast Eur Bladmoss 34 1878[lsquoUnderfamilje Oncophoreaersquo]

TYPUS Oncophorus (Brid) Brid Bryol Univ 1 389 1826

Hypodontiaceae Stech fam nov

Plantae robustae characteribus morphologicis Pottiaceis et Calymperaceis similes sedcharacteribus molecularicis separatae Bracteae perichaetiales internae e basi vaginantes subulataevel aristatae Capsula aspectu succulenta cellulae exothecii incrassatae annulus magnopereabsens Peristomii dentes breves triangulati incurvati aurantiaci leves vel infirme verrucosiCalyptra cucullata

TYPUS Hypodontium MuumlllHal Hedwigia 38 96 1899

Helicophyllales Stech amp WFrey ord nov

Plantae acrocarpae prostratae tomentosae Folia dimorpha in duas series laterales et unam seriemventralem divisa Costa percurrens Cellulae hexagonae ad subquadratae papillosae Capsula immersacupulata ad oblonga infra orificium abrupte incurvata stomata destituta Peristomium nullum Sporaeisomorphae heteropolares granulatae

TYPUS Helicophyllum Brid Bryol Univ 2 771 1827

Synopsis of the suprageneric classification of BryophytaAuthor citations are in accordance with Art 492 of the Vienna Code (McNeill et al 2006)

Subdivision Takakiophytina Stech amp WFreyClass Takakiopsida Stech amp WFrey

Order Takakiales Stech amp WFreyTakakiaceae Stech amp WFrey

Subdivision Sphagnophytina DoweldClass Sphagnopsida Schimp

Order Sphagnales Limpr

15

Sphagnaceae DumortOrder Ambuchananiales Seppelt amp HACrum

Ambuchananiaceae Seppelt amp HACrumSubdivision Bryophytina Engler

Class Andreaeopsida JHSchaffnSubclass Andreaeidae Engl

Order Andreaeales LimprAndreaeaceae Dumort

Subclass Andreaeobryidae OchyraOrder Andreaeobryales BMMurray

Andreaeobryaceae Steere amp BMMurrayClass Oedipodiopsida Goffinet amp WRBuck

Order Oedipodiales Goffinet amp WRBuckOedipodiaceae Schimp

Class Tetraphidopsida Goffinet amp WRBuckOrder Tetraphidales MFleisch

Tetraphidaceae SchimpClass Polytrichopsida Doweld

Order Polytrichales MFleischPolytrichaceae Schwaumlgr

Class Bryopsida PaxSubclass Buxbaumiidae Doweld

Order Buxbaumiales MFleischBuxbaumiaceae Schimp

Subclass Diphysciidae OchyraOrder Diphysciales MFleisch

Diphysciaceae MFleischSubclass Timmiidae Ochyra

Order Timmiales OchyraTimmiaceae Schimp

Subclass Encalyptidae Ochyra Żarnowiec amp Bednarek-OchyraOrder Encalyptales Dixon

Encalyptaceae SchimpSubclass Funariidae Ochyra

Order Funariales MFleischFunariaceae Schwaumlgr Disceliaceae Schimp

Subclass Gigaspermidae Stech amp WFreyOrder Gigaspermales Goffinet Wickett OWerner Ros AJShaw amp CJCox

Gigaspermaceae LindbSubclass Dicranidae Doweld

Order Catoscopiales Ignatov amp IgnatovaCatoscopiaceae Broth

Order Scouleriales Goffinet amp WRBuckDrummondiaceae Goffinet Scouleriaceae SPChurchill

Order Bryoxiphiales HACrum amp LEAndersonBryoxiphiaceae Besch

16

Order Grimmiales MFleischGrimmiaceae Arn Ptychomitriaceae Schimp Seligeriaceae Schimp

Order Archidiales LimprArchidiaceae Schimp

Order Mitteniales ShawMitteniaceae Broth

Order Dicranales HPhilib ex MFleischAmphidiaceae Stech Aongstroemiaceae De Not BruchiaceaeSchimp Calymperaceae Kindb Dicranaceae Schimp Dicranel-laceae Stech Ditrichaceae Limpr Erpodiaceae Broth EustichiaceaeBroth Fissidentaceae Schimp Leucobryaceae Schimp Onco-phoraceae Stech Rhachitheciaceae HRob Schistostegaceae SchimpViridivelleraceae IGStone Wardiaceae Welch

Order Pottiales MFleischEphemeraceae Schimp Hypodontiaceae Stech PleurophascaceaeBroth Pottiaceae Schimp Serpotortellaceae WDReese amp RHZander

Subclass Bryidae EnglOrder Hedwigiales Ochyra

Hedwigiaceae Schimp Rhacocarpaceae KindbOrder Helicophyllales Stech amp WFrey

Helicophyllaceae BrothOrder Bartramiales DQuandt NEBell amp Stech

Bartramiaceae SchwaumlgrOrder Splachnales Ochyra

Meesiaceae Schimp Splachnaceae Grev amp ArnOrder Bryales Limpr

Bryaceae Schwaumlgr Leptostomataceae Schwaumlgr Mniaceae SchwaumlgrPhyllodrepaniaceae Crosby Pseudoditrichaceae Steere amp ZIwatsPulchrinodaceae DQuandt NEBell amp Stech

Order Orthotrichales DixonOrthotrichaceae Arn

Order Orthodontiales NEBell AENewton amp DQuandtOrthodontiaceae Goffinet

Order Aulacomniales NEBell AENewton amp DQuandtAulacomniaceae Schimp

Order Rhizogoniales Goffinet amp WRBuckRhizogoniaceae Broth

Order Hypnodendrales NEBell AENewton amp DQuandtBraithwaiteaceae NEBell AENewton amp DQuandt Hypnodendra-ceae Broth Pterobryellaceae WRBuck amp Vitt Racopilaceae Kindb

Order Ptychomniales WRBuck CJCox AJShaw amp GoffinetPtychomniaceae MFleisch

Order Hookeriales MFleischDaltoniaceae Schimp Hookeriaceae Schimp HypopterygiaceaeMitt Leucomiaceae Broth Pilotrichaceae Kindb SaulomataceaeWRBuck CJCox AJShaw amp Goffinet Schimperobryaceae WR

17

Buck CJCox AJShaw amp GoffinetOrder Hypnales WRBuck amp Vitt

Amblystegiaceae GRoth Anomodontaceae Kindb BrachytheciaceaeSchimp Calliergonaceae Vanderpoorten Hedenaumls CJCox amp AJShaw Catagoniaceae WRBuck amp Ireland Climaciaceae KindbCryphaeaceae Schimp Echinodiaceae Broth Entodontaceae KindbFabroniaceae Schimp Fontinalaceae Schimp Helodiaceae OchyraHeterocladiaceae Ignatov amp Ignatova Hylocomiaceae MFleischHypnaceae Schimp Lembophyllaceae Broth LeptodontaceaeSchimp Lepyrodontaceae Broth Leskeaceae Schimp Leucodon-taceae Schimp Meteoriaceae Kindb Microtheciellaceae HAMillamp AJHarr Myriniaceae Schimp Myuriaceae MFleisch NeckeraceaeSchimp Orthorrhynchiaceae SHLin Phyllogoniaceae KindbPlagiotheciaceae MFleisch Pleuroziopsidaceae Ireland Prionodon-taceae Broth Pseudoleskeaceae Schimp PseudoleskeellaceaeIgnatov amp Ignatova Pterigynandraceae Schimp PterobryaceaeKindb Pylaisiaceae Schimp Pylaisiadelphaceae Goffinet amp WRBuck Regmatodontaceae Broth Rhytidiaceae Broth RigodiaceaeHACrum Rutenbergiaceae MFleisch Scorpidiaceae Ignatov ampIgnatova Sematophyllaceae Broth Sorapillaceae MFleisch Ste-reophyllaceae WRBuck amp Ireland Symphyodontaceae MFleischTheliaceae MFleisch Thuidiaceae Schimp TrachylomataceaeWRBuck amp Vitt

Acknowledgements

Sincere thanks are due to JLReveal (Ithaca) as well as WFPrudhomme van Reine and JFVeldkamp(Leiden) for comments and discussions about suprafamilial taxonomy to DQuandt (Dresden) for providingDNA from Rhacocarpus and Bartramiaceae species and to BGiesicke (Berlin) for technical assistance

References

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BELL NE amp AE NEWTON (2004) Systematic studies of non-hypnanaean pleurocarps establishinga phylogenetic framework for investigating the origins of pleurocarpy - In GOFFINET BV HOLLOWELL amp R MAGILL (eds) Molecular systematics of bryophytes Monogr Syst BotMissouri Bot Gard 98 290-319

BELL NE amp AE NEWTON (2007) Pleurocarpy in the Rhizogoniaceous grade - In NEWTONAE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolution SystematicsAssociation Special Volume Series 71 41-64

BELL NE D QUANDT TJ OBRIEN amp AE NEWTON (2007) Taxonomy and phylogeny inthe earliest diverging pleurocarps square holes and bifurcating pegs - Bryologist 110 533-560

BORSCH T KW HILU D QUANDT V WILDE C NEINHUIS amp W BARTHLOTT(2003) Non-coding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms- J Evol Biol 16 558-576

18

BUCK WR (2007) The history of pleurocarp classification two steps forward one step back - InNEWTON AE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 1-18

BUCK WR amp B GOFFINET (2000) Morphology and classification of mosses - In SHAWAJ amp B GOFFINET (eds) Bryophyte Biology pp 71-123 Cambridge University PressCambridge

CHIANG TY BA SCHAAL amp CI PENG (1998) Universal primers for amplification andsequencing a noncoding spacer between atpB and rbcL genes of chloroplast DNA - Bot Bull AcadSin 39 245-250

COX CJ B GOFFINET AE NEWTON AJ SHAW amp TAJ HEDDERSON (2000)Phylogenetic relationships among the diplolepideous-alternate mosses (Bryidae) inferred from nuclearand chloroplast DNA sequences - Bryologist 103 224-241

COX CJ B GOFFINET AJ SHAW amp SB BOLES (2004) Phylogenetic relationships amongthe mosses based on heterogeneous Bayesian analysis of multiple genes from multiple genomiccompartments - Syst Bot 29 234-250

CRANDALL-STOTLER B (1986) Morphogenesis developmental anatomy and bryophytephylogenetics contra-indications of monophyly - J Bryol 14 1-23

CROSBY MR RE MAGILL B ALLEN amp S HE (1999) A checklist of the mosses - MissouriBotanical Garden St Louis Missouri

DOWELD A (2001) Prosyllabus Tracheophytorum - GEOS Moscow i-lxxx + 110 pp

DOYLE JJ amp JL DOYLE (1990) Isolation of plant DNA from fresh tissue - Focus 12 13-15

DUFF RJ JC VILLAREAL DC CARGILL amp KS RENZAGLIA (2007) Progress andchallenges towards developing a phylogeny and classification of the hornworts - Bryologist 110214-243

FLEISCHER M (1920) Natuumlrliches System der Laubmoose - Hedwigia 61 390-400

FORREST LL EC DAVIS DG LONG BJ CRANDALL-STOTLER A CLARK ampML HOLLINGSWORTH (2006) Unraveling the evolutionary history of the liverworts (Marchantio-phyta) multiple taxa genomes and analyses - Bryologist 109 303-334

FRAHM J-P amp W FREY (1987) Moosflora 2 Aufl - UTB 1250 Stuttgart

FREY W (1977) Neue Vorstellungen uumlber die Verwandtschaftsgruppen und die Stammesgeschichteder Laubmoose - In FREY W H HURKA amp F OBERWINKLER (Hrsg) Beitraumlge zur Biologieder Pflanzen pp 117-139 Stuttgart

FREY W amp M STECH (2005) A morpho-molecular classification of the liverworts (Hepa-ticophytina Bryophyta) - Nova Hedwigia 81 55-78

FREY W M STECH amp K MEIszligNER (1999) Chloroplast DNA-relationship in palaeoaustralLopidium concinnum (Hypopterygiaceae Musci) An example of steno-evolution in mosses Studiesin austral temperate rain forest bryophytes 2 - Plant Syst Evol 218 67-75

GOFFINET B amp WR BUCK (2004) Systematics of Bryophyta (mosses) from molecules to arevised classification - In GOFFINET B V HOLLOWELL amp R MAGILL (eds) Molecularsystematics of bryophytes Monogr Syst Bot Missouri Bot Gard 98 205-239

GOFFINET B CJ COX AJ SHAW amp TAJ HEDDERSON (2001) The Bryophyta (mosses)Systematic and evolutionary inferences from an rps4 gene (cpDNA) phylogeny - Ann Bot 87191-208

GOFFINET B NJ WICKETT O WERNER RM ROS AJ SHAW amp CJ COX (2007)Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae(Bryophyta) - Ann Bot 99 747-753

19

GROTH-MALONEK M D PRUCHNER F GREWE amp V KNOOP (2005) Ancestors oftrans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosseswith vascular plants - Mol Biol Evol 22 117-125

HATTORI S amp H INOUE (1958) Preliminary report on Takakia lepidozioides - J Hattori BotLab 19 133-137

HE-NYGREacuteN X A JUSLEacuteN I AHONEN D GLENNY amp S PIIPPO (2006) Illuminating theevolutionary history of liverworts (Marchantiophyta) - towards a natural classification - Cladistics22 1-31

HEDDERSON TAJ DJ MURRAY CJ COX amp TL NOWELL (2004) Phylogeneticrelationships of haplolepideous mosses (Dicranidae) inferred from rps4 gene sequences - Syst Bot29 29-41

LA FARGE C BD MISHER JA WHEELER DP WALL K JOHANNES S SCHAFFERamp AJ SHAW (2000) Phylogenetic relationships within the haplolepideous mosses - Bryologist103 257-276

LA FARGE C AJ SHAW amp DH VITT (2002) The circumscription of the Dicranaceae(Bryopsida) based on the chloroplast regions trnL-trnF and rps4 - Syst Bot 27 435-452

MAGOMBO ZLK (2003) The phylogeny of basal peristomate mosses evidence from cpDNAand implications for peristome evolution - Syst Bot 28 24-38

MCNEILL J FR BARRIE HM BURDET V DEMOULIN DL HAWKSWORTHK MARHOLD DH NICOLSON J PRADO PC SILVA JE SKOG JH WIERSEMA ampNJ TURLAND (2006) International Code of Botanical Nomenclature (Vienna Code) - RegnumVegetabile 146 1-568

MUumlLLER K (2004) PRAP - computation of Bremer support for large data sets - Mol PhylogenetEvol 31 780-782

MUumlLLER K (2005) SeqState - primer design and sequence statistics for phylogenetic DNA datasets - Appl Bioinformatics 4 65-69

MUumlLLER K D QUANDT J MUumlLLER amp C NEINHUIS (2005) PhyDE v0992 PhylogeneticData Editor - httpwwwphydede

MURRAY BM (1988) Systematics of the Andreaeopsida (Bryophyta) two orders with links toTakakia - Nova Hedwigia Beih 90 289-336

NEWTON AE amp RS TANGNEY (eds) (2007) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 CRC Press Boca Raton 434 pp

NEWTON AE CJ COX JG DUCKETT JA WHEELER B GOFFINET TAJ HEDDER-SON amp BD MISHLER (2000) Evolution of the major moss lineages Phylogenetic analyses basedon multiple gene sequences and morphology - Bryologist 103 187-211

NEWTON AE N WIKSTROumlM NE BELL LL FORREST amp MS IGNATOV (2007)Dating the diversification of the pleurocarpous mosses - In NEWTON AE amp RS TANGNEY(eds) Pleurocarpous mosses systematics and evolution Systematics Association Special VolumeSeries 71 337-366

NIXON KC (1999) The parsimony ratchet a new method for rapid parsimony analysis - Cladistics15 407-411

OBRIEN TJ (2007) The phylogenetic distribution of pleurocarpous mosses evidence fromcpDNA sequences - In NEWTON AE amp RS TANGNEY (eds) Pleurocarpous mossessystematics and evolution Systematics Association Special Volume Series 71 19-41

OCHYRA R (2002) Nomenclatural changes in subfamilies of the Dicranaceae - CryptogamieBryol 23 345-349

20

OCHYRA R J ŻARNOWIEC amp H BEDNAREK-OCHYRA (2003) Census catalogue ofPolish mosses - Biodiv Poland 3 1-372

PEDERSEN N amp AE NEWTON (2007) Phylogenetic and morphological studies within thePtychomniales with emphasis on the evolution of dwarf males - In NEWTON AE amp RSTANGNEY (eds) Pleurocarpous mosses systematics and evolution Systematics AssociationSpecial Volume Series 71 367-392

QUANDT D amp M STECH (2005) Molecular evolution and secondary structure of the chloroplasttrnL intron in bryophytes - Mol Phylogenet Evol 36 429-443

QUANDT D K MUumlLLER amp S HUTTUNEN (2003) Characterisation of the chloroplast DNApsbT-H region and the influence of dyad symmetrical elements on phylogenetic reconstructions -Plant Biol 5 400-410

QUANDT D K MUumlLLER M STECH W FREY KW HILU amp T BORSCH (2004) Molecularevolution of the chloroplast trnL-F-region in land plants - In GOFFINET B V HOLLOWELL ampR MAGILL (eds) Molecular systematics of bryophytes Monogr Syst Bot Missouri Bot Gard98 13-37

QUANDT D NE BELL amp M STECH (2007) Unravelling the knot the Pulchrinodaceae famnov (Bryales) - In KUumlRSCHNER H T PFEIFFER amp M STECH (eds) A Festschrift to Wolf-gang Frey - a scientists life between deserts and rain forests Nova Hedwigia Beih 131 21-39

QIU Y-L Y CHO JC COX amp JD PALMER (1998) The gain of three mitochondrial intronsidentifies liverworts as the earliest land plants - Nature 394 671-674

QIU Y-L L LI B WANG Z CHEN V KNOOP M GROTH-MALONEK O DOM-BROVSKA J LEE L KENT J REST GF ESTABROOK TA HENDRY DW TAYLORCM TESTA M AMBROS B CRANDALL-STOTLER J DUFF M STECH W FREYD QUANDT amp CC DAVIS (2006) The deepest divergences in land plants inferred fromphylogenomic evidence - Proc Natl Acad Sci USA 103 15511-15516

RENZAGLIA KS S SCHUETTE RJ DUFF R LIGRONE AJ SHAW BD MISHLER ampJG DUCKETT (2007) Bryophyte phylogeny Advancing the molecular and morphological frontiers- Bryologist 110 179-213

SAMIGULLIN TH SP YACENTYUK GV DEGTYARYEVA KM VALIEJO-ROMANVK BOBROVA I CAPESIUS WF MARTIN AV TROITSKY VR FILIN amp ASANTONOV (2002) Paraphyly of bryophytes and close relationships of hornworts and vascularplants inferred from analysis of chloroplast rDNA ITS (cpITS) sequences - Arctoa 11 31-43

SANG T DJ CRAWFORD amp TF STUESSY (1997) Chloroplast DNA phylogeny reticulateevolution and biogeography of Paeonia (Paeoniaceae) - Amer J Bot 84 1120-1136

SHAW AJ amp KS RENZAGLIA (2004) Phylogeny and diversification of bryophytes - AmerJ Bot 91 1557-1581

SHAW AJ CJ COX amp B GOFFINET (2005) Global patterns of moss diversity taxonomic andmolecular inferences - Taxon 54 337-352

STECH M (1999a) A reclassification of Dicranaceae (Bryopsida) based on non-coding cpDNAsequence data - J Hattori Bot Lab 86 137-159

STECH M (1999b) A molecular systematic contribution to the position of Amphidium Schimp(Rhabdoweisiaceae Bryopsida) - Nova Hedwigia 68 291-300

STECH M (2004) Supraspecific circumscription and classification of Campylopus Brid(Dicranaceae Bryopsida) based on molecular data - Syst Bot 29 817-824

STECH M amp D QUANDT (2006) Molecular evolution of the chloroplast atpB-rbcL spacer inbryophytes - In SHARMA AK amp A SHARMA (eds) Plant Genome Biodiversity and EvolutionVol 2 Part B pp 409-431 Science Publishers Enfield New Hampshire

21

STECH M D QUANDT amp W FREY (2003) Molecular circumscription of the hornworts(Antho-cerotophyta) based on the chloroplast DNA trnL-trnF region - J Plant Res 116 389-398

STOTLER RE amp B CRANDALL-STOTLER (2005) A revised classification of theAnthocerotophyta and a checklist of the hornworts of North America north of Mexico - Bryologist108 16-26

SWOFFORD DL (2002) PAUP Phylogenetic analysis using parsimony (and other methods)version 40b10 - Sunderland MA

TABERLET P L GIELLY G PAUTOU amp J BOUVET (1991) Universal primers for amplificationof three non-coding regions of chloroplast DNA - Plant Mol Biol 17 1105-1109

TSUBOTA H Y AGENO B ESTEacuteBANEZ T YAMAGUCHI amp H DEGUCHI (2003)Molecular phylogeny of the Grimmiales (Musci) based on chloroplast rbcL sequences - Hikobia 1455-70

TSUBOTA H E DE LUNA D GONZAacuteLEZ MS IGNATOV amp H DEGUCHI (2004) Molecularphylogenetics and ordinal relationships based on analyses of a large-scale data set of 600 rbcLsequences of mosses - Hikobia 14 149-170

VITT DH (1984) Classification of the Bryopsida - In SCHUSTER RM (ed) New Manual ofBryology 2 696-759 Hattori Botanical Laboratory Nichinan Japan

VITT DH B GOFFINET amp T HEDDERSON (1998) 8 The ordinal classification of the mossesquestions and answers for the 1990s - In BATES JW NW ASHTON amp JG DUCKETT (eds)Bryology for the twenty-first century British Bryol Soc pp 113-123

Received 3 September 2007 accepted in revised form 30 October 2007

Page 7: botanica parcial 3

7

Discussion

Classification of mosses - recent progress and the current state

For a long time mosses were subdivided into three main lineages the subclassesSphagnidae Andreaeidae and Bryidae (eg Fleischer 1920 Vitt 1984 Frahm ampFrey 1987) the latter with a number of (super-)orders (eg Frey 1977) Howevermolecular data confirmed that mosses comprise a number of isolated basal lineagesrepresented by morphologically and ecologically distinct extant taxa such as TakakiaSphagnum Andreaea Andreaeobryum Oedipodium Tetraphis the Polytrichaceaeand Buxbaumia which probably have long independent phylogenetic histories (cfNewton et al 2007) As a result of molecular phylogenies and a re-evaluation ofmorphological-anatomical characters the classification of mosses has changedconsiderably in the last few years with the main lineages nowadays treated atsubdivision class and subclass levels within division Bryophyta (eg Doweld 2001Ochyra et al 2003 Goffinet amp Buck 2004 this study)

Takakia and Sphagnum are the earliest diverging moss taxa in molecular phylogenies(eg Newton et al 2000 Beckert et al 2001 Cox et al 2004 Qiu et al 2006Newton et al 2007) That Takakia is a moss and not a liverwort was confirmed byanalysis of DNA sequences and phylogenomic characters such as the distribution ofmitochondrial introns (eg Beckert et al 2001) Its taxonomic status however stillremains to be clarified On the one hand most molecular studies resolve Takakiaand Sphagnum as sister genera although only partly with high statistical supportThese molecular topologies do not support the recognition of division Takakiophytaas proposed by Crandall-Stotler (1986) One the other hand no morphologicalsynapomorphies unite Takakia with Sphagnum and significant molecular differencesseparating Takakia from all other mosses were also observed For example a regionin the plastid ITS3 is similar to that of other land plants but absent in mosses(Samigullin et al 2002) and a transition in the trnL

UAA gene changing the anticodon

to CAA was otherwise only found in leptosporangiate ferns and Ginkgo (Quandt etal 2004) Thus ldquoresolution of Sphagnum - Takakia clade may be an artifactrdquo (Shawamp Renzaglia 2004) Also Goffinet amp Buck (2004) did not unite Takakia and Sphagnumunder a formal taxonomic rank but placed them into different informal superclassesIn our opinion Takakia should be treated at the same level as Sphagnophytina andBryophytina (cf Doweld 2001) ie as a subdivision of Bryophyta However morefundamental nomenclatural changes are necessary as the family name Takakiaceaewas not validated in the original publication by Hattori amp Inoue (1958) (article411 of ICBN McNeill et al 2006) and consequently all higher taxa erected laterare invalid The corrected taxonomic treatment of Takakia is provided here withsporophytic characters included in the latin diagnosis of Takakiaceae (see taxonomy)

Within Bryophytina we recognise four morphologically and molecularly isolatedbasal lineages as separated from the arthrodontous mosses (Bryopsida) Andreaeopsida(with linear capsule dehiscence) the operculate but eperistomate Oedipodiopsida aswell as Polytrichopsida and Tetraphidopsida with nematodontous peristomes A fifthclass Andreaeobryopsida was erected by Buck amp Goffinet (2000) but re-includedin Andreaeopsida as a subclass by Ochyra et al (2003) The systematic status of

8

Andreaeobryum macrosporum Steere amp BMMurray and possible relationships withAndreaea and Takakia were discussed by Murray (1988) and summarised includingmolecular results by Shaw amp Renzaglia (2004)

On the next lower level a number of morphologically and molecularly divergentlineages are nowadays treated as subclasses of Bryopsida Buxbaumiidae andDiphysciidae are generally branching off first in molecular topologies (eg Beckertet al 2001 Magombo 2003 Cox et al 2004) followed by Timmiidae Encalyptidaeand Funariidae as well as Dicranidae (haplolepideous mosses) sister to Bryidae slThese subclasses (except Buxbaumiidae not included) are also well recognizable inthe present analysis of non-coding plastid sequences (Fig 1)

The morphologically very different Encalyptidae and Funariidae are revealed assister groups although mostly without high support in several molecular phylogenies(eg Goffinet et al 2001 Cox et al 2004 Hedderson et al 2004 Tsubota et al2003 2004) and also in the present study (Fig 1) Goffinet et al (2007) confirmedthis relationship by phylogenomic evidence namely a large (71 kb) inversion in thechloroplast genome of Funariaceae Disceliaceae and Encalyptaceae but not inGigaspermaceae Consequently the latter family was separated at ordinal level fromthe two remaining families of Funariales by Goffinet et al (2007) GigaspermalesFunariales and Encalyptales may share a common ancestor according to some butnot all molecular phylogenies (eg Goffinet et al 2001 2007 Hedderson et al2004 but not in Tsubota et al 2004) Although ontogenetic data from peristomedevelopment may support their common ancestry (Goffinet et al 2007) unambiguousmorphological synapomorphies are lacking We therefore propose to treatGigaspermaceae at subclass level within the Bryopsida (see taxonomy)

The haplolepideous mosses (Dicranidae) are clearly supported as a monophyleticlineage which obviously evolved from a diplolepideous ancestor according to theirposition in the molecular trees (eg Newton et al 2000 Tsubota et al 2003 Cox etal 2004 Goffinet amp Buck 2004) Molecular studies suitable for inferring ordinaland family level relationships within Dicranidae either focused on the haplolepideousmosses (eg Stech 1999ab 2004 LaFarge et al 2000 2002 Tsubota et al 2003Hedderson et al 2004) or included more than 15 haplolepideous taxa in analyses ofa broader range of mosses (eg Goffinet et al 2001 Tsubota et al 2004 this study)Major lineages supported by these analyses are for example Grimmiales(Grimmiaceae Ptychomitriaceae and Seligeriaceae) Leucobryaceae (incl formerDicranaceae-Campylopoideae and Paraleucobryoideae pp) Dicranaceae sstr(Dicranoideae plus former Dicnemonaceae and Paraleucobryoideae pp) Pottiaceae(incl Cinclidotaceae and Splachnobryum) and Calymperaceae (probably exclOctoblepharum) Furthermore several genera and families belong to Dicranidaewhose systematic positions have been controversial (eg Stech et al 1999b LaFarge et al 2002 Hedderson et al 2004 OBrien 2007 Quandt et al 2007 thisstudy) Amphidium Archidium Catoscopium Drummondia EphemeraceaeErpodiaceae Mittenia (cf OBrien 2007 sequences in some earlier analyses werebased on misdentified specimens) Rhachitheciaceae Schistostega Splachnobryumand Wardia On the contrary several problems remain such as the circumscriptionof Ditrichaceae and relationships of the major haplolepideous lineages in general

9

Fig 1 Strict consensus tree of 129 most parsimonious trees inferred from combined trnLUAA

intronatpB-rbcL spacer and psbA-trnH spacer sequences of 85 taxa of Bryopsida as well as Andreaearupestris (Andreaeopsida) and Pogonatum subulatum (Polytrichopsida) as outgroup representativesBootstrap support values gt50 are depicted above the branches

10

Consequently resolving the phylogeny of Dicranidae with confidence is one of themajor future challenges in moss systematics

As mentioned above Dicranaceae are monophyletic in a narrow circumscriptionaccording to molecular data In contrast to former Campylopoideae andParaleucobryoideae the status of Rhabdoweisioideae (= Oncophoroideae Ochyra2002) and Dicranelloideae needs further consideration Stech (1999ab) suggestedto recognise RhabdoweisioideaeRhabdoweisiaceae in a broad sense includingDicranoweisia Amphidium and Aongstroemia Subsequent molecular analysesconfirmed a close relationship of the genera Arctoa Cynodontium DicranoweisiaKiaeria Oncophorus Oreoweisia Oreas Rhabdoweisia and Symblepharis althoughwithout significant support (La Farge et al 2002 Tsubota et al 2003 Hedderson etal 2004) With respect to the molecular evidence available so far we propose toelevate Oncophoroideae to family level to accomodate these genera and perhapsGlyphomitrium (cf Tsubota et al 2003) whereas we consider AongstroemiaDichodontium and Diobelonella to belong to Aongstroemiaceae (cf Stech 1999a)Amphidium is neither closely related to Dicranaceae sstr nor to Oncophoroideae(La Farge et al 2002 Tsubota et al 2003 Hedderson et al 2004 Stech 2004 thisstudy) and should be treated at family level rather than placed in Dicranaceae assubfam Amphidioideae (Ochyra et al 2003) The circumscription of Dicranelloideaeis more difficult to evaluate as few representatives have been included in molecularanalyses However Dicranella heteromalla (Hedw) Schimp as well as the generaCampylopodium and Microcampylopus are clearly separated from Dicranaceae sstr(Stech 1999a 2004 La Farge et al 2002 Tsubota et al 2003 Hedderson et al2004) and consequently the subfamily deserves family status as well Finallymolecular data showed that the genus Hypodontium does not belong to Pottiaceae(Hedderson et al 2004 Tsubota et al 2004) Taxonomic conclusions have not beendrawn from these results which is made up here (see taxonomy)

All mosses with diplolepideous-alternate peristomes together with Splachnales witha diplolepideous-opposite (Funaria-type) peristome form a monophyletic group inmolecular analyses (eg Newton et al 2000 Beckert et al 2001 Goffinet et al2001 Cox et al 2004 Tsubota et al 2004 references in Table 2) Differentclassifications of this by far most species-rich group of mosses were proposed (egVitt et al 1998 Ochyra et al 2003 Goffinet amp Buck 2004) However at least someof the recognised subclasses and superorders are paraphyletic according to themolecular topologies and assigning formal ranks to all evolutionarily significantmonophyletic entities is problematic if the main taxonomic framework of Bryophytaand Bryopsida should be maintained (cf discussion in Bell et al 2007) Thereforein the present synopsis only one subclass Bryidae is recognised for all diplolepideous-alternate mosses and Splachnales This broadly defined Bryidae is subdivided into13 orders most of them resolved as monophyletic in the majority of the phylogeneticanalyses summarised in Table 2 although with different levels of statistical supportin maximum parsimony analyses To define monophyletic lineages at supraordinallevel informal node-based names may be chosen according to Bell et al (2007) Forexample the pleurocarpous mosses (pleurocarpy sensu Bell amp Newton 2007) andtheir closest acrocarpous relatives (Orthodontiales to Hypnales) were already

11

Table 2 Taxon sampling and bootstrap support (BS) for Dicranidae Bryidae and orders within theBryidae in recent phylogenetic analyses (MP only) based on combined molecular markers Markersare given in square brackets (non-coding regions in bold) numbers of included taxa in brackets ++respective clade present with ge 80 BS + clade present with lt 80 BS - clade not present no oronly one representative included

Bell amp Newton OBrien Quandt et al Bell et al this study(2004) (2007) (2007) (2007)

[rbcL rps4 [atpB atpB- [rbcL rps4 [rbcL rps4 [atpB-rbcLnad5] rbcL rbcL trnL-F nad5] trnL-F nad5] psbA-trnH

rps4 trnL-F] trnL]

Dicranidae + (2) + (4) ++ (3) (1) ++ (19)Bryidae ++ (57) + (53) ++ (52) ++ (98) ++ (58)Hedwigiales ++ (2) (1) ++ (2) ++ (2) - (3)Bartramiales ++ (2) ++ (4) ++ (4) ++ (3) - (4)Splachnales (0) ++ (2) ++ (3) ++ (2) ++ (5)Bryales - (4) - (5) ++ (18) + (17) - (8)Orthotrichales (1) ++ (3) ++ (3) ++ (2) ++ (4)Orthodontiales + (4) + (4) + (3) + (6) - (3)Aulacomniales + (6) + (7) ++ (2) + (7) + (3)Rhizogoniales ++ (13) + (8) ++ (5) ++ (14) - (3)Hypnodendrales ++ (13) + (7) ++ (4) ++ (29) ++ (6)Ptychomniales ++ (3) ++ (3) (1) ++ (4) (1)Hookeriales - (4) + (2) (1) + (2) + (8)Hypnales - (5) - (7) ++ (5) ++ (10) + (10)

summarised under the informal node based name pleurcarpids (Bell et al 2007)and can be distinguished from a basal grade of acrocarpous or cladocarpous lineages(Hedwigiales to Orthotrichales) Within the latter monophyly of BartramialesSplachnales and Orthotrichales is well-supported in all analyses including two ormore taxa except Bartramiales in the present data set (cf Fig 1) In contrast Bryalesreceive significant support less frequently (but see Bell et al 2007 Quandt et al2007) Hedwigiales are well supported if only Hedwigia (Hedwigiaceae) andRhacocarpus (Rhacocarpaceae) are included whereas the monospecific Helicophyllum(Helicophyllaceae) is not closely related to these taxa but shows affinities withBartramiales (Goffinet et al 2001 this study) With respect to the differentmorphologies of Helicophyllaceae and Bartramiaceae however the former shouldbe separated at ordinal level (see taxonomy)

Clarifying relationships of the Orthotrichales is still a difficult issue Analyses ofsingle chloroplast markers or parsimony analyses of combined markers from differentgenomes mostly indicated a close relationship either with Splachnales (eg Cox etal 2000 Newton et al 2000 Tsubota et al 2004 Quandt et al 2007) or with thepleurocarpids (Goffinet et al 2001 this study) Although none of these alternativesis well-supported the latter seems more likely with regard to the moderately tomaximally supported Orthotrichales - pleurocarpid sister group relationship in allanalyses of mitochondrial data and in likelihood analyses of combined plastidmitochondrial markers (Beckert et al 2001 Quandt et al 2007)

12

The molecular polyphyly of Rhizogoniaceae (eg Bell amp Newton 2004) was solvedby the transfer of rhizogonioid genera into broadly defined Aulacomniaceae andOrthodontiaceae (Bell et al 2007) which now include both acrocarpous andpleurocarpous taxa These systematic changes are also comprehensible by non-molecular characters such as morphological traits shared by Mesochaete andAulacomnium heterostichum (Hedw) Bruch amp Schimp or the variously reducedperistomes of Orthodontiaceae pp in contrast to the generally fully developed Bryum-type peristomes of rhizogonioid and hypnodendroid mosses (Bell et al 2007) Theposition of the solely pleurocarpous Hypnodendrales sister to the former Hypnidaeled to the recognition of the informal group core pleurocarps (Bell et al 2007)The former Hypnidae (Ptychomniales Hookeriales and Hypnales summarised ashomocostate pleurocarps) are monophyletic in most molecular analyses (eg Goffinetet al 2001 Tsubota et al 2004 Bell et al 2007) with Ptychomniales being well-supported (Pedersen amp Newton 2007 Table 2) Clarifying relationships betweenHookeriales and Hypnales and within the latter is still a challenge but recent molecularstudies seem to support a sister group relationship of both orders (Bell et al 2007present study)

Phylogenetic utility of non-coding plastid markers

Non-coding plastid markers that comprise both variable and conserved regionssuch as the trnL

UAA intron have repeatedly been shown to possess potential for

resolving relationships at high taxonomic levels (eg Borsch et al 2003 Quandtet al 2004) Both the trnL intron and atpB-rbcL spacer were characterised indetail in mosses with respect to their structure and molecular evolution (Quandt ampStech 2005 Stech amp Quandt 2006) They include conservative regions that can beunambiguosly aligned and even parts of the more variable regions can be used ifrepeats hairpin loops etc are correctly identified and adequately treated in thephylogenetic analyses (eg Quandt et al 2003 Quandt amp Stech 2005) Using theatpB-rbcL spacer alone (Stech amp Quandt 2006) relationships of the major mosslineages were largely consistent with the ldquototal evidencerdquo molecular tree of Goffinetamp Buck (2004) However in addition to general limitations that result from singlemarker analyses the use of non-coding markers may pose further problems suchas a high amount of homoplasy resulting in low resolution or low statistical supportfor many clades Therefore several recent molecular studies of relationships withinBryidae have employed both coding and non-coding markers (Table 2)Nevertheless the usefulness of analyses of combined non-coding plastid markerscannot be ruled out In fact Fig 1 and Table 2 indicate a phylogenetic signal inthe present data set as many clades are recovered that are usually also resolvedin analyses of coding or combined coding and non-coding markers Especiallywith regard to statistical support however the present analysis is inferior tothose of other recent data sets especially Bell et al (2007) and Quandt et al(2007) In addition the non-coding markers used here are of different suitabilityand even the two intergenic spacers differ considerably from each other ThepsbA-trnH spacer contributes much less to the trees resolution than the atpB-rbcL spacer first because it is much shorter and second because relatively largeparts are attributed to hairpin loops or otherwise hypervariable regions These

13

results indicate that future studies should evaluate the molecular evolution andphylogenetic potential of new markers both coding and con-coding and choosethe most suitable ones in a combined analysis to resolve the remaining uncertaintiesin moss phylogeny

Taxonomy

Takakiaceae Stech amp WFrey stat nov

Plantae virides nusquam rhizophorae sine protonemate e caudicis rhizomatis erectae Caudicesrhizomati et axes geotropi radiformes frequenter intercalariter ramificantes sine phyllidiis cumpapillis mucilaginis rostratis Caules phyllidiiferi saepe furcati Phyllidia sine lamina et costadistincta profunde 2-4(-5)-lobata pluristratosa tristicha sed torsione spiraliter disposita Filumcentralium in ambabus generationibus (axibus gametophyti et setis) adest Plantae dioicae Antheridiaet archegonia nuda Sporophytum terminale solitarium Seta persistens Capsula tortilis admaturitatem schizocarpa secus unam rimam spiralem longitudinalem dehiscens Stomata etoperculum absunt peristomium nullum Calyptra mitriformis

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiaceae SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval (Art 411)

Takakiales Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiales SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval

Takakiales SHatt amp Inoue ex RMSchust J Hattori Bot Lab 26 224 1963 nom inval (cumdescr latin)

Takakiopsida Stech amp WFrey statnov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiopsida Goffinet amp WRBuck Monogr Syst Bot Missouri Bot Gard 98 232 2004 nominval

Takakiopsida Jia et al Acta Phytotax Sin 41 350 351 2003 nom nud

Takakiopsida Wang amp Wu Fl Bryophyt Sin 8 447 2004 nom inval (cum descr latin)

Takakiophytina Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue JHattori Bot Lab 19 137 1958

Gigaspermidae Stech amp WFrey subclass nov

Plantae acrocarpae terrestres stoloniferae ramis brevibus erectis Folia unicostata cellulis laxislaevibus Capsula plerumque valde rugosa gymnostomatica vel cleistocarpa stomata cum duabuscellulis sociis Ab Funariidis et Encalyptidis charactere phylogenomico (71-kb inversio abest)separatae

14

TYPUS Gigaspermum Lindb Oumlfversigt af Foumlrhandlingar Kongl Svenska Vetenskaps-Akademien21 599 1865

Amphidiaceae Stech stat nov

Based on Dicranaceae subfam Amphidioideae Ochyra in Ochyra Zarnowiec amp Bednarek-OchyraCens Cat Polish Mosses 110 2003

TYPUS Amphidium Schimp Coroll Bryol Eur 39 1856

Amphidiaceae AJESm Moss Fl Britain Ireland 2nd ed 657 2004 nom inval descr angl

Dicranellaceae Stech stat nov

Based on Dicranaceae subfam Dicranelloideae Lindb Utkast Eur Bladmoss 33 1878[lsquoUnderfamilje Dicranelleaersquo]

TYPUS Dicranella (MuumlllHal) Schimp Coroll Bryol Eur 13 1856

Oncophoraceae Stech stat nov

Based on Dicranaceae subfam Oncophoroideae Lindb Utkast Eur Bladmoss 34 1878[lsquoUnderfamilje Oncophoreaersquo]

TYPUS Oncophorus (Brid) Brid Bryol Univ 1 389 1826

Hypodontiaceae Stech fam nov

Plantae robustae characteribus morphologicis Pottiaceis et Calymperaceis similes sedcharacteribus molecularicis separatae Bracteae perichaetiales internae e basi vaginantes subulataevel aristatae Capsula aspectu succulenta cellulae exothecii incrassatae annulus magnopereabsens Peristomii dentes breves triangulati incurvati aurantiaci leves vel infirme verrucosiCalyptra cucullata

TYPUS Hypodontium MuumlllHal Hedwigia 38 96 1899

Helicophyllales Stech amp WFrey ord nov

Plantae acrocarpae prostratae tomentosae Folia dimorpha in duas series laterales et unam seriemventralem divisa Costa percurrens Cellulae hexagonae ad subquadratae papillosae Capsula immersacupulata ad oblonga infra orificium abrupte incurvata stomata destituta Peristomium nullum Sporaeisomorphae heteropolares granulatae

TYPUS Helicophyllum Brid Bryol Univ 2 771 1827

Synopsis of the suprageneric classification of BryophytaAuthor citations are in accordance with Art 492 of the Vienna Code (McNeill et al 2006)

Subdivision Takakiophytina Stech amp WFreyClass Takakiopsida Stech amp WFrey

Order Takakiales Stech amp WFreyTakakiaceae Stech amp WFrey

Subdivision Sphagnophytina DoweldClass Sphagnopsida Schimp

Order Sphagnales Limpr

15

Sphagnaceae DumortOrder Ambuchananiales Seppelt amp HACrum

Ambuchananiaceae Seppelt amp HACrumSubdivision Bryophytina Engler

Class Andreaeopsida JHSchaffnSubclass Andreaeidae Engl

Order Andreaeales LimprAndreaeaceae Dumort

Subclass Andreaeobryidae OchyraOrder Andreaeobryales BMMurray

Andreaeobryaceae Steere amp BMMurrayClass Oedipodiopsida Goffinet amp WRBuck

Order Oedipodiales Goffinet amp WRBuckOedipodiaceae Schimp

Class Tetraphidopsida Goffinet amp WRBuckOrder Tetraphidales MFleisch

Tetraphidaceae SchimpClass Polytrichopsida Doweld

Order Polytrichales MFleischPolytrichaceae Schwaumlgr

Class Bryopsida PaxSubclass Buxbaumiidae Doweld

Order Buxbaumiales MFleischBuxbaumiaceae Schimp

Subclass Diphysciidae OchyraOrder Diphysciales MFleisch

Diphysciaceae MFleischSubclass Timmiidae Ochyra

Order Timmiales OchyraTimmiaceae Schimp

Subclass Encalyptidae Ochyra Żarnowiec amp Bednarek-OchyraOrder Encalyptales Dixon

Encalyptaceae SchimpSubclass Funariidae Ochyra

Order Funariales MFleischFunariaceae Schwaumlgr Disceliaceae Schimp

Subclass Gigaspermidae Stech amp WFreyOrder Gigaspermales Goffinet Wickett OWerner Ros AJShaw amp CJCox

Gigaspermaceae LindbSubclass Dicranidae Doweld

Order Catoscopiales Ignatov amp IgnatovaCatoscopiaceae Broth

Order Scouleriales Goffinet amp WRBuckDrummondiaceae Goffinet Scouleriaceae SPChurchill

Order Bryoxiphiales HACrum amp LEAndersonBryoxiphiaceae Besch

16

Order Grimmiales MFleischGrimmiaceae Arn Ptychomitriaceae Schimp Seligeriaceae Schimp

Order Archidiales LimprArchidiaceae Schimp

Order Mitteniales ShawMitteniaceae Broth

Order Dicranales HPhilib ex MFleischAmphidiaceae Stech Aongstroemiaceae De Not BruchiaceaeSchimp Calymperaceae Kindb Dicranaceae Schimp Dicranel-laceae Stech Ditrichaceae Limpr Erpodiaceae Broth EustichiaceaeBroth Fissidentaceae Schimp Leucobryaceae Schimp Onco-phoraceae Stech Rhachitheciaceae HRob Schistostegaceae SchimpViridivelleraceae IGStone Wardiaceae Welch

Order Pottiales MFleischEphemeraceae Schimp Hypodontiaceae Stech PleurophascaceaeBroth Pottiaceae Schimp Serpotortellaceae WDReese amp RHZander

Subclass Bryidae EnglOrder Hedwigiales Ochyra

Hedwigiaceae Schimp Rhacocarpaceae KindbOrder Helicophyllales Stech amp WFrey

Helicophyllaceae BrothOrder Bartramiales DQuandt NEBell amp Stech

Bartramiaceae SchwaumlgrOrder Splachnales Ochyra

Meesiaceae Schimp Splachnaceae Grev amp ArnOrder Bryales Limpr

Bryaceae Schwaumlgr Leptostomataceae Schwaumlgr Mniaceae SchwaumlgrPhyllodrepaniaceae Crosby Pseudoditrichaceae Steere amp ZIwatsPulchrinodaceae DQuandt NEBell amp Stech

Order Orthotrichales DixonOrthotrichaceae Arn

Order Orthodontiales NEBell AENewton amp DQuandtOrthodontiaceae Goffinet

Order Aulacomniales NEBell AENewton amp DQuandtAulacomniaceae Schimp

Order Rhizogoniales Goffinet amp WRBuckRhizogoniaceae Broth

Order Hypnodendrales NEBell AENewton amp DQuandtBraithwaiteaceae NEBell AENewton amp DQuandt Hypnodendra-ceae Broth Pterobryellaceae WRBuck amp Vitt Racopilaceae Kindb

Order Ptychomniales WRBuck CJCox AJShaw amp GoffinetPtychomniaceae MFleisch

Order Hookeriales MFleischDaltoniaceae Schimp Hookeriaceae Schimp HypopterygiaceaeMitt Leucomiaceae Broth Pilotrichaceae Kindb SaulomataceaeWRBuck CJCox AJShaw amp Goffinet Schimperobryaceae WR

17

Buck CJCox AJShaw amp GoffinetOrder Hypnales WRBuck amp Vitt

Amblystegiaceae GRoth Anomodontaceae Kindb BrachytheciaceaeSchimp Calliergonaceae Vanderpoorten Hedenaumls CJCox amp AJShaw Catagoniaceae WRBuck amp Ireland Climaciaceae KindbCryphaeaceae Schimp Echinodiaceae Broth Entodontaceae KindbFabroniaceae Schimp Fontinalaceae Schimp Helodiaceae OchyraHeterocladiaceae Ignatov amp Ignatova Hylocomiaceae MFleischHypnaceae Schimp Lembophyllaceae Broth LeptodontaceaeSchimp Lepyrodontaceae Broth Leskeaceae Schimp Leucodon-taceae Schimp Meteoriaceae Kindb Microtheciellaceae HAMillamp AJHarr Myriniaceae Schimp Myuriaceae MFleisch NeckeraceaeSchimp Orthorrhynchiaceae SHLin Phyllogoniaceae KindbPlagiotheciaceae MFleisch Pleuroziopsidaceae Ireland Prionodon-taceae Broth Pseudoleskeaceae Schimp PseudoleskeellaceaeIgnatov amp Ignatova Pterigynandraceae Schimp PterobryaceaeKindb Pylaisiaceae Schimp Pylaisiadelphaceae Goffinet amp WRBuck Regmatodontaceae Broth Rhytidiaceae Broth RigodiaceaeHACrum Rutenbergiaceae MFleisch Scorpidiaceae Ignatov ampIgnatova Sematophyllaceae Broth Sorapillaceae MFleisch Ste-reophyllaceae WRBuck amp Ireland Symphyodontaceae MFleischTheliaceae MFleisch Thuidiaceae Schimp TrachylomataceaeWRBuck amp Vitt

Acknowledgements

Sincere thanks are due to JLReveal (Ithaca) as well as WFPrudhomme van Reine and JFVeldkamp(Leiden) for comments and discussions about suprafamilial taxonomy to DQuandt (Dresden) for providingDNA from Rhacocarpus and Bartramiaceae species and to BGiesicke (Berlin) for technical assistance

References

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BELL NE amp AE NEWTON (2004) Systematic studies of non-hypnanaean pleurocarps establishinga phylogenetic framework for investigating the origins of pleurocarpy - In GOFFINET BV HOLLOWELL amp R MAGILL (eds) Molecular systematics of bryophytes Monogr Syst BotMissouri Bot Gard 98 290-319

BELL NE amp AE NEWTON (2007) Pleurocarpy in the Rhizogoniaceous grade - In NEWTONAE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolution SystematicsAssociation Special Volume Series 71 41-64

BELL NE D QUANDT TJ OBRIEN amp AE NEWTON (2007) Taxonomy and phylogeny inthe earliest diverging pleurocarps square holes and bifurcating pegs - Bryologist 110 533-560

BORSCH T KW HILU D QUANDT V WILDE C NEINHUIS amp W BARTHLOTT(2003) Non-coding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms- J Evol Biol 16 558-576

18

BUCK WR (2007) The history of pleurocarp classification two steps forward one step back - InNEWTON AE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 1-18

BUCK WR amp B GOFFINET (2000) Morphology and classification of mosses - In SHAWAJ amp B GOFFINET (eds) Bryophyte Biology pp 71-123 Cambridge University PressCambridge

CHIANG TY BA SCHAAL amp CI PENG (1998) Universal primers for amplification andsequencing a noncoding spacer between atpB and rbcL genes of chloroplast DNA - Bot Bull AcadSin 39 245-250

COX CJ B GOFFINET AE NEWTON AJ SHAW amp TAJ HEDDERSON (2000)Phylogenetic relationships among the diplolepideous-alternate mosses (Bryidae) inferred from nuclearand chloroplast DNA sequences - Bryologist 103 224-241

COX CJ B GOFFINET AJ SHAW amp SB BOLES (2004) Phylogenetic relationships amongthe mosses based on heterogeneous Bayesian analysis of multiple genes from multiple genomiccompartments - Syst Bot 29 234-250

CRANDALL-STOTLER B (1986) Morphogenesis developmental anatomy and bryophytephylogenetics contra-indications of monophyly - J Bryol 14 1-23

CROSBY MR RE MAGILL B ALLEN amp S HE (1999) A checklist of the mosses - MissouriBotanical Garden St Louis Missouri

DOWELD A (2001) Prosyllabus Tracheophytorum - GEOS Moscow i-lxxx + 110 pp

DOYLE JJ amp JL DOYLE (1990) Isolation of plant DNA from fresh tissue - Focus 12 13-15

DUFF RJ JC VILLAREAL DC CARGILL amp KS RENZAGLIA (2007) Progress andchallenges towards developing a phylogeny and classification of the hornworts - Bryologist 110214-243

FLEISCHER M (1920) Natuumlrliches System der Laubmoose - Hedwigia 61 390-400

FORREST LL EC DAVIS DG LONG BJ CRANDALL-STOTLER A CLARK ampML HOLLINGSWORTH (2006) Unraveling the evolutionary history of the liverworts (Marchantio-phyta) multiple taxa genomes and analyses - Bryologist 109 303-334

FRAHM J-P amp W FREY (1987) Moosflora 2 Aufl - UTB 1250 Stuttgart

FREY W (1977) Neue Vorstellungen uumlber die Verwandtschaftsgruppen und die Stammesgeschichteder Laubmoose - In FREY W H HURKA amp F OBERWINKLER (Hrsg) Beitraumlge zur Biologieder Pflanzen pp 117-139 Stuttgart

FREY W amp M STECH (2005) A morpho-molecular classification of the liverworts (Hepa-ticophytina Bryophyta) - Nova Hedwigia 81 55-78

FREY W M STECH amp K MEIszligNER (1999) Chloroplast DNA-relationship in palaeoaustralLopidium concinnum (Hypopterygiaceae Musci) An example of steno-evolution in mosses Studiesin austral temperate rain forest bryophytes 2 - Plant Syst Evol 218 67-75

GOFFINET B amp WR BUCK (2004) Systematics of Bryophyta (mosses) from molecules to arevised classification - In GOFFINET B V HOLLOWELL amp R MAGILL (eds) Molecularsystematics of bryophytes Monogr Syst Bot Missouri Bot Gard 98 205-239

GOFFINET B CJ COX AJ SHAW amp TAJ HEDDERSON (2001) The Bryophyta (mosses)Systematic and evolutionary inferences from an rps4 gene (cpDNA) phylogeny - Ann Bot 87191-208

GOFFINET B NJ WICKETT O WERNER RM ROS AJ SHAW amp CJ COX (2007)Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae(Bryophyta) - Ann Bot 99 747-753

19

GROTH-MALONEK M D PRUCHNER F GREWE amp V KNOOP (2005) Ancestors oftrans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosseswith vascular plants - Mol Biol Evol 22 117-125

HATTORI S amp H INOUE (1958) Preliminary report on Takakia lepidozioides - J Hattori BotLab 19 133-137

HE-NYGREacuteN X A JUSLEacuteN I AHONEN D GLENNY amp S PIIPPO (2006) Illuminating theevolutionary history of liverworts (Marchantiophyta) - towards a natural classification - Cladistics22 1-31

HEDDERSON TAJ DJ MURRAY CJ COX amp TL NOWELL (2004) Phylogeneticrelationships of haplolepideous mosses (Dicranidae) inferred from rps4 gene sequences - Syst Bot29 29-41

LA FARGE C BD MISHER JA WHEELER DP WALL K JOHANNES S SCHAFFERamp AJ SHAW (2000) Phylogenetic relationships within the haplolepideous mosses - Bryologist103 257-276

LA FARGE C AJ SHAW amp DH VITT (2002) The circumscription of the Dicranaceae(Bryopsida) based on the chloroplast regions trnL-trnF and rps4 - Syst Bot 27 435-452

MAGOMBO ZLK (2003) The phylogeny of basal peristomate mosses evidence from cpDNAand implications for peristome evolution - Syst Bot 28 24-38

MCNEILL J FR BARRIE HM BURDET V DEMOULIN DL HAWKSWORTHK MARHOLD DH NICOLSON J PRADO PC SILVA JE SKOG JH WIERSEMA ampNJ TURLAND (2006) International Code of Botanical Nomenclature (Vienna Code) - RegnumVegetabile 146 1-568

MUumlLLER K (2004) PRAP - computation of Bremer support for large data sets - Mol PhylogenetEvol 31 780-782

MUumlLLER K (2005) SeqState - primer design and sequence statistics for phylogenetic DNA datasets - Appl Bioinformatics 4 65-69

MUumlLLER K D QUANDT J MUumlLLER amp C NEINHUIS (2005) PhyDE v0992 PhylogeneticData Editor - httpwwwphydede

MURRAY BM (1988) Systematics of the Andreaeopsida (Bryophyta) two orders with links toTakakia - Nova Hedwigia Beih 90 289-336

NEWTON AE amp RS TANGNEY (eds) (2007) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 CRC Press Boca Raton 434 pp

NEWTON AE CJ COX JG DUCKETT JA WHEELER B GOFFINET TAJ HEDDER-SON amp BD MISHLER (2000) Evolution of the major moss lineages Phylogenetic analyses basedon multiple gene sequences and morphology - Bryologist 103 187-211

NEWTON AE N WIKSTROumlM NE BELL LL FORREST amp MS IGNATOV (2007)Dating the diversification of the pleurocarpous mosses - In NEWTON AE amp RS TANGNEY(eds) Pleurocarpous mosses systematics and evolution Systematics Association Special VolumeSeries 71 337-366

NIXON KC (1999) The parsimony ratchet a new method for rapid parsimony analysis - Cladistics15 407-411

OBRIEN TJ (2007) The phylogenetic distribution of pleurocarpous mosses evidence fromcpDNA sequences - In NEWTON AE amp RS TANGNEY (eds) Pleurocarpous mossessystematics and evolution Systematics Association Special Volume Series 71 19-41

OCHYRA R (2002) Nomenclatural changes in subfamilies of the Dicranaceae - CryptogamieBryol 23 345-349

20

OCHYRA R J ŻARNOWIEC amp H BEDNAREK-OCHYRA (2003) Census catalogue ofPolish mosses - Biodiv Poland 3 1-372

PEDERSEN N amp AE NEWTON (2007) Phylogenetic and morphological studies within thePtychomniales with emphasis on the evolution of dwarf males - In NEWTON AE amp RSTANGNEY (eds) Pleurocarpous mosses systematics and evolution Systematics AssociationSpecial Volume Series 71 367-392

QUANDT D amp M STECH (2005) Molecular evolution and secondary structure of the chloroplasttrnL intron in bryophytes - Mol Phylogenet Evol 36 429-443

QUANDT D K MUumlLLER amp S HUTTUNEN (2003) Characterisation of the chloroplast DNApsbT-H region and the influence of dyad symmetrical elements on phylogenetic reconstructions -Plant Biol 5 400-410

QUANDT D K MUumlLLER M STECH W FREY KW HILU amp T BORSCH (2004) Molecularevolution of the chloroplast trnL-F-region in land plants - In GOFFINET B V HOLLOWELL ampR MAGILL (eds) Molecular systematics of bryophytes Monogr Syst Bot Missouri Bot Gard98 13-37

QUANDT D NE BELL amp M STECH (2007) Unravelling the knot the Pulchrinodaceae famnov (Bryales) - In KUumlRSCHNER H T PFEIFFER amp M STECH (eds) A Festschrift to Wolf-gang Frey - a scientists life between deserts and rain forests Nova Hedwigia Beih 131 21-39

QIU Y-L Y CHO JC COX amp JD PALMER (1998) The gain of three mitochondrial intronsidentifies liverworts as the earliest land plants - Nature 394 671-674

QIU Y-L L LI B WANG Z CHEN V KNOOP M GROTH-MALONEK O DOM-BROVSKA J LEE L KENT J REST GF ESTABROOK TA HENDRY DW TAYLORCM TESTA M AMBROS B CRANDALL-STOTLER J DUFF M STECH W FREYD QUANDT amp CC DAVIS (2006) The deepest divergences in land plants inferred fromphylogenomic evidence - Proc Natl Acad Sci USA 103 15511-15516

RENZAGLIA KS S SCHUETTE RJ DUFF R LIGRONE AJ SHAW BD MISHLER ampJG DUCKETT (2007) Bryophyte phylogeny Advancing the molecular and morphological frontiers- Bryologist 110 179-213

SAMIGULLIN TH SP YACENTYUK GV DEGTYARYEVA KM VALIEJO-ROMANVK BOBROVA I CAPESIUS WF MARTIN AV TROITSKY VR FILIN amp ASANTONOV (2002) Paraphyly of bryophytes and close relationships of hornworts and vascularplants inferred from analysis of chloroplast rDNA ITS (cpITS) sequences - Arctoa 11 31-43

SANG T DJ CRAWFORD amp TF STUESSY (1997) Chloroplast DNA phylogeny reticulateevolution and biogeography of Paeonia (Paeoniaceae) - Amer J Bot 84 1120-1136

SHAW AJ amp KS RENZAGLIA (2004) Phylogeny and diversification of bryophytes - AmerJ Bot 91 1557-1581

SHAW AJ CJ COX amp B GOFFINET (2005) Global patterns of moss diversity taxonomic andmolecular inferences - Taxon 54 337-352

STECH M (1999a) A reclassification of Dicranaceae (Bryopsida) based on non-coding cpDNAsequence data - J Hattori Bot Lab 86 137-159

STECH M (1999b) A molecular systematic contribution to the position of Amphidium Schimp(Rhabdoweisiaceae Bryopsida) - Nova Hedwigia 68 291-300

STECH M (2004) Supraspecific circumscription and classification of Campylopus Brid(Dicranaceae Bryopsida) based on molecular data - Syst Bot 29 817-824

STECH M amp D QUANDT (2006) Molecular evolution of the chloroplast atpB-rbcL spacer inbryophytes - In SHARMA AK amp A SHARMA (eds) Plant Genome Biodiversity and EvolutionVol 2 Part B pp 409-431 Science Publishers Enfield New Hampshire

21

STECH M D QUANDT amp W FREY (2003) Molecular circumscription of the hornworts(Antho-cerotophyta) based on the chloroplast DNA trnL-trnF region - J Plant Res 116 389-398

STOTLER RE amp B CRANDALL-STOTLER (2005) A revised classification of theAnthocerotophyta and a checklist of the hornworts of North America north of Mexico - Bryologist108 16-26

SWOFFORD DL (2002) PAUP Phylogenetic analysis using parsimony (and other methods)version 40b10 - Sunderland MA

TABERLET P L GIELLY G PAUTOU amp J BOUVET (1991) Universal primers for amplificationof three non-coding regions of chloroplast DNA - Plant Mol Biol 17 1105-1109

TSUBOTA H Y AGENO B ESTEacuteBANEZ T YAMAGUCHI amp H DEGUCHI (2003)Molecular phylogeny of the Grimmiales (Musci) based on chloroplast rbcL sequences - Hikobia 1455-70

TSUBOTA H E DE LUNA D GONZAacuteLEZ MS IGNATOV amp H DEGUCHI (2004) Molecularphylogenetics and ordinal relationships based on analyses of a large-scale data set of 600 rbcLsequences of mosses - Hikobia 14 149-170

VITT DH (1984) Classification of the Bryopsida - In SCHUSTER RM (ed) New Manual ofBryology 2 696-759 Hattori Botanical Laboratory Nichinan Japan

VITT DH B GOFFINET amp T HEDDERSON (1998) 8 The ordinal classification of the mossesquestions and answers for the 1990s - In BATES JW NW ASHTON amp JG DUCKETT (eds)Bryology for the twenty-first century British Bryol Soc pp 113-123

Received 3 September 2007 accepted in revised form 30 October 2007

Page 8: botanica parcial 3

8

Andreaeobryum macrosporum Steere amp BMMurray and possible relationships withAndreaea and Takakia were discussed by Murray (1988) and summarised includingmolecular results by Shaw amp Renzaglia (2004)

On the next lower level a number of morphologically and molecularly divergentlineages are nowadays treated as subclasses of Bryopsida Buxbaumiidae andDiphysciidae are generally branching off first in molecular topologies (eg Beckertet al 2001 Magombo 2003 Cox et al 2004) followed by Timmiidae Encalyptidaeand Funariidae as well as Dicranidae (haplolepideous mosses) sister to Bryidae slThese subclasses (except Buxbaumiidae not included) are also well recognizable inthe present analysis of non-coding plastid sequences (Fig 1)

The morphologically very different Encalyptidae and Funariidae are revealed assister groups although mostly without high support in several molecular phylogenies(eg Goffinet et al 2001 Cox et al 2004 Hedderson et al 2004 Tsubota et al2003 2004) and also in the present study (Fig 1) Goffinet et al (2007) confirmedthis relationship by phylogenomic evidence namely a large (71 kb) inversion in thechloroplast genome of Funariaceae Disceliaceae and Encalyptaceae but not inGigaspermaceae Consequently the latter family was separated at ordinal level fromthe two remaining families of Funariales by Goffinet et al (2007) GigaspermalesFunariales and Encalyptales may share a common ancestor according to some butnot all molecular phylogenies (eg Goffinet et al 2001 2007 Hedderson et al2004 but not in Tsubota et al 2004) Although ontogenetic data from peristomedevelopment may support their common ancestry (Goffinet et al 2007) unambiguousmorphological synapomorphies are lacking We therefore propose to treatGigaspermaceae at subclass level within the Bryopsida (see taxonomy)

The haplolepideous mosses (Dicranidae) are clearly supported as a monophyleticlineage which obviously evolved from a diplolepideous ancestor according to theirposition in the molecular trees (eg Newton et al 2000 Tsubota et al 2003 Cox etal 2004 Goffinet amp Buck 2004) Molecular studies suitable for inferring ordinaland family level relationships within Dicranidae either focused on the haplolepideousmosses (eg Stech 1999ab 2004 LaFarge et al 2000 2002 Tsubota et al 2003Hedderson et al 2004) or included more than 15 haplolepideous taxa in analyses ofa broader range of mosses (eg Goffinet et al 2001 Tsubota et al 2004 this study)Major lineages supported by these analyses are for example Grimmiales(Grimmiaceae Ptychomitriaceae and Seligeriaceae) Leucobryaceae (incl formerDicranaceae-Campylopoideae and Paraleucobryoideae pp) Dicranaceae sstr(Dicranoideae plus former Dicnemonaceae and Paraleucobryoideae pp) Pottiaceae(incl Cinclidotaceae and Splachnobryum) and Calymperaceae (probably exclOctoblepharum) Furthermore several genera and families belong to Dicranidaewhose systematic positions have been controversial (eg Stech et al 1999b LaFarge et al 2002 Hedderson et al 2004 OBrien 2007 Quandt et al 2007 thisstudy) Amphidium Archidium Catoscopium Drummondia EphemeraceaeErpodiaceae Mittenia (cf OBrien 2007 sequences in some earlier analyses werebased on misdentified specimens) Rhachitheciaceae Schistostega Splachnobryumand Wardia On the contrary several problems remain such as the circumscriptionof Ditrichaceae and relationships of the major haplolepideous lineages in general

9

Fig 1 Strict consensus tree of 129 most parsimonious trees inferred from combined trnLUAA

intronatpB-rbcL spacer and psbA-trnH spacer sequences of 85 taxa of Bryopsida as well as Andreaearupestris (Andreaeopsida) and Pogonatum subulatum (Polytrichopsida) as outgroup representativesBootstrap support values gt50 are depicted above the branches

10

Consequently resolving the phylogeny of Dicranidae with confidence is one of themajor future challenges in moss systematics

As mentioned above Dicranaceae are monophyletic in a narrow circumscriptionaccording to molecular data In contrast to former Campylopoideae andParaleucobryoideae the status of Rhabdoweisioideae (= Oncophoroideae Ochyra2002) and Dicranelloideae needs further consideration Stech (1999ab) suggestedto recognise RhabdoweisioideaeRhabdoweisiaceae in a broad sense includingDicranoweisia Amphidium and Aongstroemia Subsequent molecular analysesconfirmed a close relationship of the genera Arctoa Cynodontium DicranoweisiaKiaeria Oncophorus Oreoweisia Oreas Rhabdoweisia and Symblepharis althoughwithout significant support (La Farge et al 2002 Tsubota et al 2003 Hedderson etal 2004) With respect to the molecular evidence available so far we propose toelevate Oncophoroideae to family level to accomodate these genera and perhapsGlyphomitrium (cf Tsubota et al 2003) whereas we consider AongstroemiaDichodontium and Diobelonella to belong to Aongstroemiaceae (cf Stech 1999a)Amphidium is neither closely related to Dicranaceae sstr nor to Oncophoroideae(La Farge et al 2002 Tsubota et al 2003 Hedderson et al 2004 Stech 2004 thisstudy) and should be treated at family level rather than placed in Dicranaceae assubfam Amphidioideae (Ochyra et al 2003) The circumscription of Dicranelloideaeis more difficult to evaluate as few representatives have been included in molecularanalyses However Dicranella heteromalla (Hedw) Schimp as well as the generaCampylopodium and Microcampylopus are clearly separated from Dicranaceae sstr(Stech 1999a 2004 La Farge et al 2002 Tsubota et al 2003 Hedderson et al2004) and consequently the subfamily deserves family status as well Finallymolecular data showed that the genus Hypodontium does not belong to Pottiaceae(Hedderson et al 2004 Tsubota et al 2004) Taxonomic conclusions have not beendrawn from these results which is made up here (see taxonomy)

All mosses with diplolepideous-alternate peristomes together with Splachnales witha diplolepideous-opposite (Funaria-type) peristome form a monophyletic group inmolecular analyses (eg Newton et al 2000 Beckert et al 2001 Goffinet et al2001 Cox et al 2004 Tsubota et al 2004 references in Table 2) Differentclassifications of this by far most species-rich group of mosses were proposed (egVitt et al 1998 Ochyra et al 2003 Goffinet amp Buck 2004) However at least someof the recognised subclasses and superorders are paraphyletic according to themolecular topologies and assigning formal ranks to all evolutionarily significantmonophyletic entities is problematic if the main taxonomic framework of Bryophytaand Bryopsida should be maintained (cf discussion in Bell et al 2007) Thereforein the present synopsis only one subclass Bryidae is recognised for all diplolepideous-alternate mosses and Splachnales This broadly defined Bryidae is subdivided into13 orders most of them resolved as monophyletic in the majority of the phylogeneticanalyses summarised in Table 2 although with different levels of statistical supportin maximum parsimony analyses To define monophyletic lineages at supraordinallevel informal node-based names may be chosen according to Bell et al (2007) Forexample the pleurocarpous mosses (pleurocarpy sensu Bell amp Newton 2007) andtheir closest acrocarpous relatives (Orthodontiales to Hypnales) were already

11

Table 2 Taxon sampling and bootstrap support (BS) for Dicranidae Bryidae and orders within theBryidae in recent phylogenetic analyses (MP only) based on combined molecular markers Markersare given in square brackets (non-coding regions in bold) numbers of included taxa in brackets ++respective clade present with ge 80 BS + clade present with lt 80 BS - clade not present no oronly one representative included

Bell amp Newton OBrien Quandt et al Bell et al this study(2004) (2007) (2007) (2007)

[rbcL rps4 [atpB atpB- [rbcL rps4 [rbcL rps4 [atpB-rbcLnad5] rbcL rbcL trnL-F nad5] trnL-F nad5] psbA-trnH

rps4 trnL-F] trnL]

Dicranidae + (2) + (4) ++ (3) (1) ++ (19)Bryidae ++ (57) + (53) ++ (52) ++ (98) ++ (58)Hedwigiales ++ (2) (1) ++ (2) ++ (2) - (3)Bartramiales ++ (2) ++ (4) ++ (4) ++ (3) - (4)Splachnales (0) ++ (2) ++ (3) ++ (2) ++ (5)Bryales - (4) - (5) ++ (18) + (17) - (8)Orthotrichales (1) ++ (3) ++ (3) ++ (2) ++ (4)Orthodontiales + (4) + (4) + (3) + (6) - (3)Aulacomniales + (6) + (7) ++ (2) + (7) + (3)Rhizogoniales ++ (13) + (8) ++ (5) ++ (14) - (3)Hypnodendrales ++ (13) + (7) ++ (4) ++ (29) ++ (6)Ptychomniales ++ (3) ++ (3) (1) ++ (4) (1)Hookeriales - (4) + (2) (1) + (2) + (8)Hypnales - (5) - (7) ++ (5) ++ (10) + (10)

summarised under the informal node based name pleurcarpids (Bell et al 2007)and can be distinguished from a basal grade of acrocarpous or cladocarpous lineages(Hedwigiales to Orthotrichales) Within the latter monophyly of BartramialesSplachnales and Orthotrichales is well-supported in all analyses including two ormore taxa except Bartramiales in the present data set (cf Fig 1) In contrast Bryalesreceive significant support less frequently (but see Bell et al 2007 Quandt et al2007) Hedwigiales are well supported if only Hedwigia (Hedwigiaceae) andRhacocarpus (Rhacocarpaceae) are included whereas the monospecific Helicophyllum(Helicophyllaceae) is not closely related to these taxa but shows affinities withBartramiales (Goffinet et al 2001 this study) With respect to the differentmorphologies of Helicophyllaceae and Bartramiaceae however the former shouldbe separated at ordinal level (see taxonomy)

Clarifying relationships of the Orthotrichales is still a difficult issue Analyses ofsingle chloroplast markers or parsimony analyses of combined markers from differentgenomes mostly indicated a close relationship either with Splachnales (eg Cox etal 2000 Newton et al 2000 Tsubota et al 2004 Quandt et al 2007) or with thepleurocarpids (Goffinet et al 2001 this study) Although none of these alternativesis well-supported the latter seems more likely with regard to the moderately tomaximally supported Orthotrichales - pleurocarpid sister group relationship in allanalyses of mitochondrial data and in likelihood analyses of combined plastidmitochondrial markers (Beckert et al 2001 Quandt et al 2007)

12

The molecular polyphyly of Rhizogoniaceae (eg Bell amp Newton 2004) was solvedby the transfer of rhizogonioid genera into broadly defined Aulacomniaceae andOrthodontiaceae (Bell et al 2007) which now include both acrocarpous andpleurocarpous taxa These systematic changes are also comprehensible by non-molecular characters such as morphological traits shared by Mesochaete andAulacomnium heterostichum (Hedw) Bruch amp Schimp or the variously reducedperistomes of Orthodontiaceae pp in contrast to the generally fully developed Bryum-type peristomes of rhizogonioid and hypnodendroid mosses (Bell et al 2007) Theposition of the solely pleurocarpous Hypnodendrales sister to the former Hypnidaeled to the recognition of the informal group core pleurocarps (Bell et al 2007)The former Hypnidae (Ptychomniales Hookeriales and Hypnales summarised ashomocostate pleurocarps) are monophyletic in most molecular analyses (eg Goffinetet al 2001 Tsubota et al 2004 Bell et al 2007) with Ptychomniales being well-supported (Pedersen amp Newton 2007 Table 2) Clarifying relationships betweenHookeriales and Hypnales and within the latter is still a challenge but recent molecularstudies seem to support a sister group relationship of both orders (Bell et al 2007present study)

Phylogenetic utility of non-coding plastid markers

Non-coding plastid markers that comprise both variable and conserved regionssuch as the trnL

UAA intron have repeatedly been shown to possess potential for

resolving relationships at high taxonomic levels (eg Borsch et al 2003 Quandtet al 2004) Both the trnL intron and atpB-rbcL spacer were characterised indetail in mosses with respect to their structure and molecular evolution (Quandt ampStech 2005 Stech amp Quandt 2006) They include conservative regions that can beunambiguosly aligned and even parts of the more variable regions can be used ifrepeats hairpin loops etc are correctly identified and adequately treated in thephylogenetic analyses (eg Quandt et al 2003 Quandt amp Stech 2005) Using theatpB-rbcL spacer alone (Stech amp Quandt 2006) relationships of the major mosslineages were largely consistent with the ldquototal evidencerdquo molecular tree of Goffinetamp Buck (2004) However in addition to general limitations that result from singlemarker analyses the use of non-coding markers may pose further problems suchas a high amount of homoplasy resulting in low resolution or low statistical supportfor many clades Therefore several recent molecular studies of relationships withinBryidae have employed both coding and non-coding markers (Table 2)Nevertheless the usefulness of analyses of combined non-coding plastid markerscannot be ruled out In fact Fig 1 and Table 2 indicate a phylogenetic signal inthe present data set as many clades are recovered that are usually also resolvedin analyses of coding or combined coding and non-coding markers Especiallywith regard to statistical support however the present analysis is inferior tothose of other recent data sets especially Bell et al (2007) and Quandt et al(2007) In addition the non-coding markers used here are of different suitabilityand even the two intergenic spacers differ considerably from each other ThepsbA-trnH spacer contributes much less to the trees resolution than the atpB-rbcL spacer first because it is much shorter and second because relatively largeparts are attributed to hairpin loops or otherwise hypervariable regions These

13

results indicate that future studies should evaluate the molecular evolution andphylogenetic potential of new markers both coding and con-coding and choosethe most suitable ones in a combined analysis to resolve the remaining uncertaintiesin moss phylogeny

Taxonomy

Takakiaceae Stech amp WFrey stat nov

Plantae virides nusquam rhizophorae sine protonemate e caudicis rhizomatis erectae Caudicesrhizomati et axes geotropi radiformes frequenter intercalariter ramificantes sine phyllidiis cumpapillis mucilaginis rostratis Caules phyllidiiferi saepe furcati Phyllidia sine lamina et costadistincta profunde 2-4(-5)-lobata pluristratosa tristicha sed torsione spiraliter disposita Filumcentralium in ambabus generationibus (axibus gametophyti et setis) adest Plantae dioicae Antheridiaet archegonia nuda Sporophytum terminale solitarium Seta persistens Capsula tortilis admaturitatem schizocarpa secus unam rimam spiralem longitudinalem dehiscens Stomata etoperculum absunt peristomium nullum Calyptra mitriformis

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiaceae SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval (Art 411)

Takakiales Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiales SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval

Takakiales SHatt amp Inoue ex RMSchust J Hattori Bot Lab 26 224 1963 nom inval (cumdescr latin)

Takakiopsida Stech amp WFrey statnov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiopsida Goffinet amp WRBuck Monogr Syst Bot Missouri Bot Gard 98 232 2004 nominval

Takakiopsida Jia et al Acta Phytotax Sin 41 350 351 2003 nom nud

Takakiopsida Wang amp Wu Fl Bryophyt Sin 8 447 2004 nom inval (cum descr latin)

Takakiophytina Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue JHattori Bot Lab 19 137 1958

Gigaspermidae Stech amp WFrey subclass nov

Plantae acrocarpae terrestres stoloniferae ramis brevibus erectis Folia unicostata cellulis laxislaevibus Capsula plerumque valde rugosa gymnostomatica vel cleistocarpa stomata cum duabuscellulis sociis Ab Funariidis et Encalyptidis charactere phylogenomico (71-kb inversio abest)separatae

14

TYPUS Gigaspermum Lindb Oumlfversigt af Foumlrhandlingar Kongl Svenska Vetenskaps-Akademien21 599 1865

Amphidiaceae Stech stat nov

Based on Dicranaceae subfam Amphidioideae Ochyra in Ochyra Zarnowiec amp Bednarek-OchyraCens Cat Polish Mosses 110 2003

TYPUS Amphidium Schimp Coroll Bryol Eur 39 1856

Amphidiaceae AJESm Moss Fl Britain Ireland 2nd ed 657 2004 nom inval descr angl

Dicranellaceae Stech stat nov

Based on Dicranaceae subfam Dicranelloideae Lindb Utkast Eur Bladmoss 33 1878[lsquoUnderfamilje Dicranelleaersquo]

TYPUS Dicranella (MuumlllHal) Schimp Coroll Bryol Eur 13 1856

Oncophoraceae Stech stat nov

Based on Dicranaceae subfam Oncophoroideae Lindb Utkast Eur Bladmoss 34 1878[lsquoUnderfamilje Oncophoreaersquo]

TYPUS Oncophorus (Brid) Brid Bryol Univ 1 389 1826

Hypodontiaceae Stech fam nov

Plantae robustae characteribus morphologicis Pottiaceis et Calymperaceis similes sedcharacteribus molecularicis separatae Bracteae perichaetiales internae e basi vaginantes subulataevel aristatae Capsula aspectu succulenta cellulae exothecii incrassatae annulus magnopereabsens Peristomii dentes breves triangulati incurvati aurantiaci leves vel infirme verrucosiCalyptra cucullata

TYPUS Hypodontium MuumlllHal Hedwigia 38 96 1899

Helicophyllales Stech amp WFrey ord nov

Plantae acrocarpae prostratae tomentosae Folia dimorpha in duas series laterales et unam seriemventralem divisa Costa percurrens Cellulae hexagonae ad subquadratae papillosae Capsula immersacupulata ad oblonga infra orificium abrupte incurvata stomata destituta Peristomium nullum Sporaeisomorphae heteropolares granulatae

TYPUS Helicophyllum Brid Bryol Univ 2 771 1827

Synopsis of the suprageneric classification of BryophytaAuthor citations are in accordance with Art 492 of the Vienna Code (McNeill et al 2006)

Subdivision Takakiophytina Stech amp WFreyClass Takakiopsida Stech amp WFrey

Order Takakiales Stech amp WFreyTakakiaceae Stech amp WFrey

Subdivision Sphagnophytina DoweldClass Sphagnopsida Schimp

Order Sphagnales Limpr

15

Sphagnaceae DumortOrder Ambuchananiales Seppelt amp HACrum

Ambuchananiaceae Seppelt amp HACrumSubdivision Bryophytina Engler

Class Andreaeopsida JHSchaffnSubclass Andreaeidae Engl

Order Andreaeales LimprAndreaeaceae Dumort

Subclass Andreaeobryidae OchyraOrder Andreaeobryales BMMurray

Andreaeobryaceae Steere amp BMMurrayClass Oedipodiopsida Goffinet amp WRBuck

Order Oedipodiales Goffinet amp WRBuckOedipodiaceae Schimp

Class Tetraphidopsida Goffinet amp WRBuckOrder Tetraphidales MFleisch

Tetraphidaceae SchimpClass Polytrichopsida Doweld

Order Polytrichales MFleischPolytrichaceae Schwaumlgr

Class Bryopsida PaxSubclass Buxbaumiidae Doweld

Order Buxbaumiales MFleischBuxbaumiaceae Schimp

Subclass Diphysciidae OchyraOrder Diphysciales MFleisch

Diphysciaceae MFleischSubclass Timmiidae Ochyra

Order Timmiales OchyraTimmiaceae Schimp

Subclass Encalyptidae Ochyra Żarnowiec amp Bednarek-OchyraOrder Encalyptales Dixon

Encalyptaceae SchimpSubclass Funariidae Ochyra

Order Funariales MFleischFunariaceae Schwaumlgr Disceliaceae Schimp

Subclass Gigaspermidae Stech amp WFreyOrder Gigaspermales Goffinet Wickett OWerner Ros AJShaw amp CJCox

Gigaspermaceae LindbSubclass Dicranidae Doweld

Order Catoscopiales Ignatov amp IgnatovaCatoscopiaceae Broth

Order Scouleriales Goffinet amp WRBuckDrummondiaceae Goffinet Scouleriaceae SPChurchill

Order Bryoxiphiales HACrum amp LEAndersonBryoxiphiaceae Besch

16

Order Grimmiales MFleischGrimmiaceae Arn Ptychomitriaceae Schimp Seligeriaceae Schimp

Order Archidiales LimprArchidiaceae Schimp

Order Mitteniales ShawMitteniaceae Broth

Order Dicranales HPhilib ex MFleischAmphidiaceae Stech Aongstroemiaceae De Not BruchiaceaeSchimp Calymperaceae Kindb Dicranaceae Schimp Dicranel-laceae Stech Ditrichaceae Limpr Erpodiaceae Broth EustichiaceaeBroth Fissidentaceae Schimp Leucobryaceae Schimp Onco-phoraceae Stech Rhachitheciaceae HRob Schistostegaceae SchimpViridivelleraceae IGStone Wardiaceae Welch

Order Pottiales MFleischEphemeraceae Schimp Hypodontiaceae Stech PleurophascaceaeBroth Pottiaceae Schimp Serpotortellaceae WDReese amp RHZander

Subclass Bryidae EnglOrder Hedwigiales Ochyra

Hedwigiaceae Schimp Rhacocarpaceae KindbOrder Helicophyllales Stech amp WFrey

Helicophyllaceae BrothOrder Bartramiales DQuandt NEBell amp Stech

Bartramiaceae SchwaumlgrOrder Splachnales Ochyra

Meesiaceae Schimp Splachnaceae Grev amp ArnOrder Bryales Limpr

Bryaceae Schwaumlgr Leptostomataceae Schwaumlgr Mniaceae SchwaumlgrPhyllodrepaniaceae Crosby Pseudoditrichaceae Steere amp ZIwatsPulchrinodaceae DQuandt NEBell amp Stech

Order Orthotrichales DixonOrthotrichaceae Arn

Order Orthodontiales NEBell AENewton amp DQuandtOrthodontiaceae Goffinet

Order Aulacomniales NEBell AENewton amp DQuandtAulacomniaceae Schimp

Order Rhizogoniales Goffinet amp WRBuckRhizogoniaceae Broth

Order Hypnodendrales NEBell AENewton amp DQuandtBraithwaiteaceae NEBell AENewton amp DQuandt Hypnodendra-ceae Broth Pterobryellaceae WRBuck amp Vitt Racopilaceae Kindb

Order Ptychomniales WRBuck CJCox AJShaw amp GoffinetPtychomniaceae MFleisch

Order Hookeriales MFleischDaltoniaceae Schimp Hookeriaceae Schimp HypopterygiaceaeMitt Leucomiaceae Broth Pilotrichaceae Kindb SaulomataceaeWRBuck CJCox AJShaw amp Goffinet Schimperobryaceae WR

17

Buck CJCox AJShaw amp GoffinetOrder Hypnales WRBuck amp Vitt

Amblystegiaceae GRoth Anomodontaceae Kindb BrachytheciaceaeSchimp Calliergonaceae Vanderpoorten Hedenaumls CJCox amp AJShaw Catagoniaceae WRBuck amp Ireland Climaciaceae KindbCryphaeaceae Schimp Echinodiaceae Broth Entodontaceae KindbFabroniaceae Schimp Fontinalaceae Schimp Helodiaceae OchyraHeterocladiaceae Ignatov amp Ignatova Hylocomiaceae MFleischHypnaceae Schimp Lembophyllaceae Broth LeptodontaceaeSchimp Lepyrodontaceae Broth Leskeaceae Schimp Leucodon-taceae Schimp Meteoriaceae Kindb Microtheciellaceae HAMillamp AJHarr Myriniaceae Schimp Myuriaceae MFleisch NeckeraceaeSchimp Orthorrhynchiaceae SHLin Phyllogoniaceae KindbPlagiotheciaceae MFleisch Pleuroziopsidaceae Ireland Prionodon-taceae Broth Pseudoleskeaceae Schimp PseudoleskeellaceaeIgnatov amp Ignatova Pterigynandraceae Schimp PterobryaceaeKindb Pylaisiaceae Schimp Pylaisiadelphaceae Goffinet amp WRBuck Regmatodontaceae Broth Rhytidiaceae Broth RigodiaceaeHACrum Rutenbergiaceae MFleisch Scorpidiaceae Ignatov ampIgnatova Sematophyllaceae Broth Sorapillaceae MFleisch Ste-reophyllaceae WRBuck amp Ireland Symphyodontaceae MFleischTheliaceae MFleisch Thuidiaceae Schimp TrachylomataceaeWRBuck amp Vitt

Acknowledgements

Sincere thanks are due to JLReveal (Ithaca) as well as WFPrudhomme van Reine and JFVeldkamp(Leiden) for comments and discussions about suprafamilial taxonomy to DQuandt (Dresden) for providingDNA from Rhacocarpus and Bartramiaceae species and to BGiesicke (Berlin) for technical assistance

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BELL NE amp AE NEWTON (2004) Systematic studies of non-hypnanaean pleurocarps establishinga phylogenetic framework for investigating the origins of pleurocarpy - In GOFFINET BV HOLLOWELL amp R MAGILL (eds) Molecular systematics of bryophytes Monogr Syst BotMissouri Bot Gard 98 290-319

BELL NE amp AE NEWTON (2007) Pleurocarpy in the Rhizogoniaceous grade - In NEWTONAE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolution SystematicsAssociation Special Volume Series 71 41-64

BELL NE D QUANDT TJ OBRIEN amp AE NEWTON (2007) Taxonomy and phylogeny inthe earliest diverging pleurocarps square holes and bifurcating pegs - Bryologist 110 533-560

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18

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FREY W amp M STECH (2005) A morpho-molecular classification of the liverworts (Hepa-ticophytina Bryophyta) - Nova Hedwigia 81 55-78

FREY W M STECH amp K MEIszligNER (1999) Chloroplast DNA-relationship in palaeoaustralLopidium concinnum (Hypopterygiaceae Musci) An example of steno-evolution in mosses Studiesin austral temperate rain forest bryophytes 2 - Plant Syst Evol 218 67-75

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GOFFINET B CJ COX AJ SHAW amp TAJ HEDDERSON (2001) The Bryophyta (mosses)Systematic and evolutionary inferences from an rps4 gene (cpDNA) phylogeny - Ann Bot 87191-208

GOFFINET B NJ WICKETT O WERNER RM ROS AJ SHAW amp CJ COX (2007)Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae(Bryophyta) - Ann Bot 99 747-753

19

GROTH-MALONEK M D PRUCHNER F GREWE amp V KNOOP (2005) Ancestors oftrans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosseswith vascular plants - Mol Biol Evol 22 117-125

HATTORI S amp H INOUE (1958) Preliminary report on Takakia lepidozioides - J Hattori BotLab 19 133-137

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LA FARGE C BD MISHER JA WHEELER DP WALL K JOHANNES S SCHAFFERamp AJ SHAW (2000) Phylogenetic relationships within the haplolepideous mosses - Bryologist103 257-276

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MCNEILL J FR BARRIE HM BURDET V DEMOULIN DL HAWKSWORTHK MARHOLD DH NICOLSON J PRADO PC SILVA JE SKOG JH WIERSEMA ampNJ TURLAND (2006) International Code of Botanical Nomenclature (Vienna Code) - RegnumVegetabile 146 1-568

MUumlLLER K (2004) PRAP - computation of Bremer support for large data sets - Mol PhylogenetEvol 31 780-782

MUumlLLER K (2005) SeqState - primer design and sequence statistics for phylogenetic DNA datasets - Appl Bioinformatics 4 65-69

MUumlLLER K D QUANDT J MUumlLLER amp C NEINHUIS (2005) PhyDE v0992 PhylogeneticData Editor - httpwwwphydede

MURRAY BM (1988) Systematics of the Andreaeopsida (Bryophyta) two orders with links toTakakia - Nova Hedwigia Beih 90 289-336

NEWTON AE amp RS TANGNEY (eds) (2007) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 CRC Press Boca Raton 434 pp

NEWTON AE CJ COX JG DUCKETT JA WHEELER B GOFFINET TAJ HEDDER-SON amp BD MISHLER (2000) Evolution of the major moss lineages Phylogenetic analyses basedon multiple gene sequences and morphology - Bryologist 103 187-211

NEWTON AE N WIKSTROumlM NE BELL LL FORREST amp MS IGNATOV (2007)Dating the diversification of the pleurocarpous mosses - In NEWTON AE amp RS TANGNEY(eds) Pleurocarpous mosses systematics and evolution Systematics Association Special VolumeSeries 71 337-366

NIXON KC (1999) The parsimony ratchet a new method for rapid parsimony analysis - Cladistics15 407-411

OBRIEN TJ (2007) The phylogenetic distribution of pleurocarpous mosses evidence fromcpDNA sequences - In NEWTON AE amp RS TANGNEY (eds) Pleurocarpous mossessystematics and evolution Systematics Association Special Volume Series 71 19-41

OCHYRA R (2002) Nomenclatural changes in subfamilies of the Dicranaceae - CryptogamieBryol 23 345-349

20

OCHYRA R J ŻARNOWIEC amp H BEDNAREK-OCHYRA (2003) Census catalogue ofPolish mosses - Biodiv Poland 3 1-372

PEDERSEN N amp AE NEWTON (2007) Phylogenetic and morphological studies within thePtychomniales with emphasis on the evolution of dwarf males - In NEWTON AE amp RSTANGNEY (eds) Pleurocarpous mosses systematics and evolution Systematics AssociationSpecial Volume Series 71 367-392

QUANDT D amp M STECH (2005) Molecular evolution and secondary structure of the chloroplasttrnL intron in bryophytes - Mol Phylogenet Evol 36 429-443

QUANDT D K MUumlLLER amp S HUTTUNEN (2003) Characterisation of the chloroplast DNApsbT-H region and the influence of dyad symmetrical elements on phylogenetic reconstructions -Plant Biol 5 400-410

QUANDT D K MUumlLLER M STECH W FREY KW HILU amp T BORSCH (2004) Molecularevolution of the chloroplast trnL-F-region in land plants - In GOFFINET B V HOLLOWELL ampR MAGILL (eds) Molecular systematics of bryophytes Monogr Syst Bot Missouri Bot Gard98 13-37

QUANDT D NE BELL amp M STECH (2007) Unravelling the knot the Pulchrinodaceae famnov (Bryales) - In KUumlRSCHNER H T PFEIFFER amp M STECH (eds) A Festschrift to Wolf-gang Frey - a scientists life between deserts and rain forests Nova Hedwigia Beih 131 21-39

QIU Y-L Y CHO JC COX amp JD PALMER (1998) The gain of three mitochondrial intronsidentifies liverworts as the earliest land plants - Nature 394 671-674

QIU Y-L L LI B WANG Z CHEN V KNOOP M GROTH-MALONEK O DOM-BROVSKA J LEE L KENT J REST GF ESTABROOK TA HENDRY DW TAYLORCM TESTA M AMBROS B CRANDALL-STOTLER J DUFF M STECH W FREYD QUANDT amp CC DAVIS (2006) The deepest divergences in land plants inferred fromphylogenomic evidence - Proc Natl Acad Sci USA 103 15511-15516

RENZAGLIA KS S SCHUETTE RJ DUFF R LIGRONE AJ SHAW BD MISHLER ampJG DUCKETT (2007) Bryophyte phylogeny Advancing the molecular and morphological frontiers- Bryologist 110 179-213

SAMIGULLIN TH SP YACENTYUK GV DEGTYARYEVA KM VALIEJO-ROMANVK BOBROVA I CAPESIUS WF MARTIN AV TROITSKY VR FILIN amp ASANTONOV (2002) Paraphyly of bryophytes and close relationships of hornworts and vascularplants inferred from analysis of chloroplast rDNA ITS (cpITS) sequences - Arctoa 11 31-43

SANG T DJ CRAWFORD amp TF STUESSY (1997) Chloroplast DNA phylogeny reticulateevolution and biogeography of Paeonia (Paeoniaceae) - Amer J Bot 84 1120-1136

SHAW AJ amp KS RENZAGLIA (2004) Phylogeny and diversification of bryophytes - AmerJ Bot 91 1557-1581

SHAW AJ CJ COX amp B GOFFINET (2005) Global patterns of moss diversity taxonomic andmolecular inferences - Taxon 54 337-352

STECH M (1999a) A reclassification of Dicranaceae (Bryopsida) based on non-coding cpDNAsequence data - J Hattori Bot Lab 86 137-159

STECH M (1999b) A molecular systematic contribution to the position of Amphidium Schimp(Rhabdoweisiaceae Bryopsida) - Nova Hedwigia 68 291-300

STECH M (2004) Supraspecific circumscription and classification of Campylopus Brid(Dicranaceae Bryopsida) based on molecular data - Syst Bot 29 817-824

STECH M amp D QUANDT (2006) Molecular evolution of the chloroplast atpB-rbcL spacer inbryophytes - In SHARMA AK amp A SHARMA (eds) Plant Genome Biodiversity and EvolutionVol 2 Part B pp 409-431 Science Publishers Enfield New Hampshire

21

STECH M D QUANDT amp W FREY (2003) Molecular circumscription of the hornworts(Antho-cerotophyta) based on the chloroplast DNA trnL-trnF region - J Plant Res 116 389-398

STOTLER RE amp B CRANDALL-STOTLER (2005) A revised classification of theAnthocerotophyta and a checklist of the hornworts of North America north of Mexico - Bryologist108 16-26

SWOFFORD DL (2002) PAUP Phylogenetic analysis using parsimony (and other methods)version 40b10 - Sunderland MA

TABERLET P L GIELLY G PAUTOU amp J BOUVET (1991) Universal primers for amplificationof three non-coding regions of chloroplast DNA - Plant Mol Biol 17 1105-1109

TSUBOTA H Y AGENO B ESTEacuteBANEZ T YAMAGUCHI amp H DEGUCHI (2003)Molecular phylogeny of the Grimmiales (Musci) based on chloroplast rbcL sequences - Hikobia 1455-70

TSUBOTA H E DE LUNA D GONZAacuteLEZ MS IGNATOV amp H DEGUCHI (2004) Molecularphylogenetics and ordinal relationships based on analyses of a large-scale data set of 600 rbcLsequences of mosses - Hikobia 14 149-170

VITT DH (1984) Classification of the Bryopsida - In SCHUSTER RM (ed) New Manual ofBryology 2 696-759 Hattori Botanical Laboratory Nichinan Japan

VITT DH B GOFFINET amp T HEDDERSON (1998) 8 The ordinal classification of the mossesquestions and answers for the 1990s - In BATES JW NW ASHTON amp JG DUCKETT (eds)Bryology for the twenty-first century British Bryol Soc pp 113-123

Received 3 September 2007 accepted in revised form 30 October 2007

Page 9: botanica parcial 3

9

Fig 1 Strict consensus tree of 129 most parsimonious trees inferred from combined trnLUAA

intronatpB-rbcL spacer and psbA-trnH spacer sequences of 85 taxa of Bryopsida as well as Andreaearupestris (Andreaeopsida) and Pogonatum subulatum (Polytrichopsida) as outgroup representativesBootstrap support values gt50 are depicted above the branches

10

Consequently resolving the phylogeny of Dicranidae with confidence is one of themajor future challenges in moss systematics

As mentioned above Dicranaceae are monophyletic in a narrow circumscriptionaccording to molecular data In contrast to former Campylopoideae andParaleucobryoideae the status of Rhabdoweisioideae (= Oncophoroideae Ochyra2002) and Dicranelloideae needs further consideration Stech (1999ab) suggestedto recognise RhabdoweisioideaeRhabdoweisiaceae in a broad sense includingDicranoweisia Amphidium and Aongstroemia Subsequent molecular analysesconfirmed a close relationship of the genera Arctoa Cynodontium DicranoweisiaKiaeria Oncophorus Oreoweisia Oreas Rhabdoweisia and Symblepharis althoughwithout significant support (La Farge et al 2002 Tsubota et al 2003 Hedderson etal 2004) With respect to the molecular evidence available so far we propose toelevate Oncophoroideae to family level to accomodate these genera and perhapsGlyphomitrium (cf Tsubota et al 2003) whereas we consider AongstroemiaDichodontium and Diobelonella to belong to Aongstroemiaceae (cf Stech 1999a)Amphidium is neither closely related to Dicranaceae sstr nor to Oncophoroideae(La Farge et al 2002 Tsubota et al 2003 Hedderson et al 2004 Stech 2004 thisstudy) and should be treated at family level rather than placed in Dicranaceae assubfam Amphidioideae (Ochyra et al 2003) The circumscription of Dicranelloideaeis more difficult to evaluate as few representatives have been included in molecularanalyses However Dicranella heteromalla (Hedw) Schimp as well as the generaCampylopodium and Microcampylopus are clearly separated from Dicranaceae sstr(Stech 1999a 2004 La Farge et al 2002 Tsubota et al 2003 Hedderson et al2004) and consequently the subfamily deserves family status as well Finallymolecular data showed that the genus Hypodontium does not belong to Pottiaceae(Hedderson et al 2004 Tsubota et al 2004) Taxonomic conclusions have not beendrawn from these results which is made up here (see taxonomy)

All mosses with diplolepideous-alternate peristomes together with Splachnales witha diplolepideous-opposite (Funaria-type) peristome form a monophyletic group inmolecular analyses (eg Newton et al 2000 Beckert et al 2001 Goffinet et al2001 Cox et al 2004 Tsubota et al 2004 references in Table 2) Differentclassifications of this by far most species-rich group of mosses were proposed (egVitt et al 1998 Ochyra et al 2003 Goffinet amp Buck 2004) However at least someof the recognised subclasses and superorders are paraphyletic according to themolecular topologies and assigning formal ranks to all evolutionarily significantmonophyletic entities is problematic if the main taxonomic framework of Bryophytaand Bryopsida should be maintained (cf discussion in Bell et al 2007) Thereforein the present synopsis only one subclass Bryidae is recognised for all diplolepideous-alternate mosses and Splachnales This broadly defined Bryidae is subdivided into13 orders most of them resolved as monophyletic in the majority of the phylogeneticanalyses summarised in Table 2 although with different levels of statistical supportin maximum parsimony analyses To define monophyletic lineages at supraordinallevel informal node-based names may be chosen according to Bell et al (2007) Forexample the pleurocarpous mosses (pleurocarpy sensu Bell amp Newton 2007) andtheir closest acrocarpous relatives (Orthodontiales to Hypnales) were already

11

Table 2 Taxon sampling and bootstrap support (BS) for Dicranidae Bryidae and orders within theBryidae in recent phylogenetic analyses (MP only) based on combined molecular markers Markersare given in square brackets (non-coding regions in bold) numbers of included taxa in brackets ++respective clade present with ge 80 BS + clade present with lt 80 BS - clade not present no oronly one representative included

Bell amp Newton OBrien Quandt et al Bell et al this study(2004) (2007) (2007) (2007)

[rbcL rps4 [atpB atpB- [rbcL rps4 [rbcL rps4 [atpB-rbcLnad5] rbcL rbcL trnL-F nad5] trnL-F nad5] psbA-trnH

rps4 trnL-F] trnL]

Dicranidae + (2) + (4) ++ (3) (1) ++ (19)Bryidae ++ (57) + (53) ++ (52) ++ (98) ++ (58)Hedwigiales ++ (2) (1) ++ (2) ++ (2) - (3)Bartramiales ++ (2) ++ (4) ++ (4) ++ (3) - (4)Splachnales (0) ++ (2) ++ (3) ++ (2) ++ (5)Bryales - (4) - (5) ++ (18) + (17) - (8)Orthotrichales (1) ++ (3) ++ (3) ++ (2) ++ (4)Orthodontiales + (4) + (4) + (3) + (6) - (3)Aulacomniales + (6) + (7) ++ (2) + (7) + (3)Rhizogoniales ++ (13) + (8) ++ (5) ++ (14) - (3)Hypnodendrales ++ (13) + (7) ++ (4) ++ (29) ++ (6)Ptychomniales ++ (3) ++ (3) (1) ++ (4) (1)Hookeriales - (4) + (2) (1) + (2) + (8)Hypnales - (5) - (7) ++ (5) ++ (10) + (10)

summarised under the informal node based name pleurcarpids (Bell et al 2007)and can be distinguished from a basal grade of acrocarpous or cladocarpous lineages(Hedwigiales to Orthotrichales) Within the latter monophyly of BartramialesSplachnales and Orthotrichales is well-supported in all analyses including two ormore taxa except Bartramiales in the present data set (cf Fig 1) In contrast Bryalesreceive significant support less frequently (but see Bell et al 2007 Quandt et al2007) Hedwigiales are well supported if only Hedwigia (Hedwigiaceae) andRhacocarpus (Rhacocarpaceae) are included whereas the monospecific Helicophyllum(Helicophyllaceae) is not closely related to these taxa but shows affinities withBartramiales (Goffinet et al 2001 this study) With respect to the differentmorphologies of Helicophyllaceae and Bartramiaceae however the former shouldbe separated at ordinal level (see taxonomy)

Clarifying relationships of the Orthotrichales is still a difficult issue Analyses ofsingle chloroplast markers or parsimony analyses of combined markers from differentgenomes mostly indicated a close relationship either with Splachnales (eg Cox etal 2000 Newton et al 2000 Tsubota et al 2004 Quandt et al 2007) or with thepleurocarpids (Goffinet et al 2001 this study) Although none of these alternativesis well-supported the latter seems more likely with regard to the moderately tomaximally supported Orthotrichales - pleurocarpid sister group relationship in allanalyses of mitochondrial data and in likelihood analyses of combined plastidmitochondrial markers (Beckert et al 2001 Quandt et al 2007)

12

The molecular polyphyly of Rhizogoniaceae (eg Bell amp Newton 2004) was solvedby the transfer of rhizogonioid genera into broadly defined Aulacomniaceae andOrthodontiaceae (Bell et al 2007) which now include both acrocarpous andpleurocarpous taxa These systematic changes are also comprehensible by non-molecular characters such as morphological traits shared by Mesochaete andAulacomnium heterostichum (Hedw) Bruch amp Schimp or the variously reducedperistomes of Orthodontiaceae pp in contrast to the generally fully developed Bryum-type peristomes of rhizogonioid and hypnodendroid mosses (Bell et al 2007) Theposition of the solely pleurocarpous Hypnodendrales sister to the former Hypnidaeled to the recognition of the informal group core pleurocarps (Bell et al 2007)The former Hypnidae (Ptychomniales Hookeriales and Hypnales summarised ashomocostate pleurocarps) are monophyletic in most molecular analyses (eg Goffinetet al 2001 Tsubota et al 2004 Bell et al 2007) with Ptychomniales being well-supported (Pedersen amp Newton 2007 Table 2) Clarifying relationships betweenHookeriales and Hypnales and within the latter is still a challenge but recent molecularstudies seem to support a sister group relationship of both orders (Bell et al 2007present study)

Phylogenetic utility of non-coding plastid markers

Non-coding plastid markers that comprise both variable and conserved regionssuch as the trnL

UAA intron have repeatedly been shown to possess potential for

resolving relationships at high taxonomic levels (eg Borsch et al 2003 Quandtet al 2004) Both the trnL intron and atpB-rbcL spacer were characterised indetail in mosses with respect to their structure and molecular evolution (Quandt ampStech 2005 Stech amp Quandt 2006) They include conservative regions that can beunambiguosly aligned and even parts of the more variable regions can be used ifrepeats hairpin loops etc are correctly identified and adequately treated in thephylogenetic analyses (eg Quandt et al 2003 Quandt amp Stech 2005) Using theatpB-rbcL spacer alone (Stech amp Quandt 2006) relationships of the major mosslineages were largely consistent with the ldquototal evidencerdquo molecular tree of Goffinetamp Buck (2004) However in addition to general limitations that result from singlemarker analyses the use of non-coding markers may pose further problems suchas a high amount of homoplasy resulting in low resolution or low statistical supportfor many clades Therefore several recent molecular studies of relationships withinBryidae have employed both coding and non-coding markers (Table 2)Nevertheless the usefulness of analyses of combined non-coding plastid markerscannot be ruled out In fact Fig 1 and Table 2 indicate a phylogenetic signal inthe present data set as many clades are recovered that are usually also resolvedin analyses of coding or combined coding and non-coding markers Especiallywith regard to statistical support however the present analysis is inferior tothose of other recent data sets especially Bell et al (2007) and Quandt et al(2007) In addition the non-coding markers used here are of different suitabilityand even the two intergenic spacers differ considerably from each other ThepsbA-trnH spacer contributes much less to the trees resolution than the atpB-rbcL spacer first because it is much shorter and second because relatively largeparts are attributed to hairpin loops or otherwise hypervariable regions These

13

results indicate that future studies should evaluate the molecular evolution andphylogenetic potential of new markers both coding and con-coding and choosethe most suitable ones in a combined analysis to resolve the remaining uncertaintiesin moss phylogeny

Taxonomy

Takakiaceae Stech amp WFrey stat nov

Plantae virides nusquam rhizophorae sine protonemate e caudicis rhizomatis erectae Caudicesrhizomati et axes geotropi radiformes frequenter intercalariter ramificantes sine phyllidiis cumpapillis mucilaginis rostratis Caules phyllidiiferi saepe furcati Phyllidia sine lamina et costadistincta profunde 2-4(-5)-lobata pluristratosa tristicha sed torsione spiraliter disposita Filumcentralium in ambabus generationibus (axibus gametophyti et setis) adest Plantae dioicae Antheridiaet archegonia nuda Sporophytum terminale solitarium Seta persistens Capsula tortilis admaturitatem schizocarpa secus unam rimam spiralem longitudinalem dehiscens Stomata etoperculum absunt peristomium nullum Calyptra mitriformis

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiaceae SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval (Art 411)

Takakiales Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiales SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval

Takakiales SHatt amp Inoue ex RMSchust J Hattori Bot Lab 26 224 1963 nom inval (cumdescr latin)

Takakiopsida Stech amp WFrey statnov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiopsida Goffinet amp WRBuck Monogr Syst Bot Missouri Bot Gard 98 232 2004 nominval

Takakiopsida Jia et al Acta Phytotax Sin 41 350 351 2003 nom nud

Takakiopsida Wang amp Wu Fl Bryophyt Sin 8 447 2004 nom inval (cum descr latin)

Takakiophytina Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue JHattori Bot Lab 19 137 1958

Gigaspermidae Stech amp WFrey subclass nov

Plantae acrocarpae terrestres stoloniferae ramis brevibus erectis Folia unicostata cellulis laxislaevibus Capsula plerumque valde rugosa gymnostomatica vel cleistocarpa stomata cum duabuscellulis sociis Ab Funariidis et Encalyptidis charactere phylogenomico (71-kb inversio abest)separatae

14

TYPUS Gigaspermum Lindb Oumlfversigt af Foumlrhandlingar Kongl Svenska Vetenskaps-Akademien21 599 1865

Amphidiaceae Stech stat nov

Based on Dicranaceae subfam Amphidioideae Ochyra in Ochyra Zarnowiec amp Bednarek-OchyraCens Cat Polish Mosses 110 2003

TYPUS Amphidium Schimp Coroll Bryol Eur 39 1856

Amphidiaceae AJESm Moss Fl Britain Ireland 2nd ed 657 2004 nom inval descr angl

Dicranellaceae Stech stat nov

Based on Dicranaceae subfam Dicranelloideae Lindb Utkast Eur Bladmoss 33 1878[lsquoUnderfamilje Dicranelleaersquo]

TYPUS Dicranella (MuumlllHal) Schimp Coroll Bryol Eur 13 1856

Oncophoraceae Stech stat nov

Based on Dicranaceae subfam Oncophoroideae Lindb Utkast Eur Bladmoss 34 1878[lsquoUnderfamilje Oncophoreaersquo]

TYPUS Oncophorus (Brid) Brid Bryol Univ 1 389 1826

Hypodontiaceae Stech fam nov

Plantae robustae characteribus morphologicis Pottiaceis et Calymperaceis similes sedcharacteribus molecularicis separatae Bracteae perichaetiales internae e basi vaginantes subulataevel aristatae Capsula aspectu succulenta cellulae exothecii incrassatae annulus magnopereabsens Peristomii dentes breves triangulati incurvati aurantiaci leves vel infirme verrucosiCalyptra cucullata

TYPUS Hypodontium MuumlllHal Hedwigia 38 96 1899

Helicophyllales Stech amp WFrey ord nov

Plantae acrocarpae prostratae tomentosae Folia dimorpha in duas series laterales et unam seriemventralem divisa Costa percurrens Cellulae hexagonae ad subquadratae papillosae Capsula immersacupulata ad oblonga infra orificium abrupte incurvata stomata destituta Peristomium nullum Sporaeisomorphae heteropolares granulatae

TYPUS Helicophyllum Brid Bryol Univ 2 771 1827

Synopsis of the suprageneric classification of BryophytaAuthor citations are in accordance with Art 492 of the Vienna Code (McNeill et al 2006)

Subdivision Takakiophytina Stech amp WFreyClass Takakiopsida Stech amp WFrey

Order Takakiales Stech amp WFreyTakakiaceae Stech amp WFrey

Subdivision Sphagnophytina DoweldClass Sphagnopsida Schimp

Order Sphagnales Limpr

15

Sphagnaceae DumortOrder Ambuchananiales Seppelt amp HACrum

Ambuchananiaceae Seppelt amp HACrumSubdivision Bryophytina Engler

Class Andreaeopsida JHSchaffnSubclass Andreaeidae Engl

Order Andreaeales LimprAndreaeaceae Dumort

Subclass Andreaeobryidae OchyraOrder Andreaeobryales BMMurray

Andreaeobryaceae Steere amp BMMurrayClass Oedipodiopsida Goffinet amp WRBuck

Order Oedipodiales Goffinet amp WRBuckOedipodiaceae Schimp

Class Tetraphidopsida Goffinet amp WRBuckOrder Tetraphidales MFleisch

Tetraphidaceae SchimpClass Polytrichopsida Doweld

Order Polytrichales MFleischPolytrichaceae Schwaumlgr

Class Bryopsida PaxSubclass Buxbaumiidae Doweld

Order Buxbaumiales MFleischBuxbaumiaceae Schimp

Subclass Diphysciidae OchyraOrder Diphysciales MFleisch

Diphysciaceae MFleischSubclass Timmiidae Ochyra

Order Timmiales OchyraTimmiaceae Schimp

Subclass Encalyptidae Ochyra Żarnowiec amp Bednarek-OchyraOrder Encalyptales Dixon

Encalyptaceae SchimpSubclass Funariidae Ochyra

Order Funariales MFleischFunariaceae Schwaumlgr Disceliaceae Schimp

Subclass Gigaspermidae Stech amp WFreyOrder Gigaspermales Goffinet Wickett OWerner Ros AJShaw amp CJCox

Gigaspermaceae LindbSubclass Dicranidae Doweld

Order Catoscopiales Ignatov amp IgnatovaCatoscopiaceae Broth

Order Scouleriales Goffinet amp WRBuckDrummondiaceae Goffinet Scouleriaceae SPChurchill

Order Bryoxiphiales HACrum amp LEAndersonBryoxiphiaceae Besch

16

Order Grimmiales MFleischGrimmiaceae Arn Ptychomitriaceae Schimp Seligeriaceae Schimp

Order Archidiales LimprArchidiaceae Schimp

Order Mitteniales ShawMitteniaceae Broth

Order Dicranales HPhilib ex MFleischAmphidiaceae Stech Aongstroemiaceae De Not BruchiaceaeSchimp Calymperaceae Kindb Dicranaceae Schimp Dicranel-laceae Stech Ditrichaceae Limpr Erpodiaceae Broth EustichiaceaeBroth Fissidentaceae Schimp Leucobryaceae Schimp Onco-phoraceae Stech Rhachitheciaceae HRob Schistostegaceae SchimpViridivelleraceae IGStone Wardiaceae Welch

Order Pottiales MFleischEphemeraceae Schimp Hypodontiaceae Stech PleurophascaceaeBroth Pottiaceae Schimp Serpotortellaceae WDReese amp RHZander

Subclass Bryidae EnglOrder Hedwigiales Ochyra

Hedwigiaceae Schimp Rhacocarpaceae KindbOrder Helicophyllales Stech amp WFrey

Helicophyllaceae BrothOrder Bartramiales DQuandt NEBell amp Stech

Bartramiaceae SchwaumlgrOrder Splachnales Ochyra

Meesiaceae Schimp Splachnaceae Grev amp ArnOrder Bryales Limpr

Bryaceae Schwaumlgr Leptostomataceae Schwaumlgr Mniaceae SchwaumlgrPhyllodrepaniaceae Crosby Pseudoditrichaceae Steere amp ZIwatsPulchrinodaceae DQuandt NEBell amp Stech

Order Orthotrichales DixonOrthotrichaceae Arn

Order Orthodontiales NEBell AENewton amp DQuandtOrthodontiaceae Goffinet

Order Aulacomniales NEBell AENewton amp DQuandtAulacomniaceae Schimp

Order Rhizogoniales Goffinet amp WRBuckRhizogoniaceae Broth

Order Hypnodendrales NEBell AENewton amp DQuandtBraithwaiteaceae NEBell AENewton amp DQuandt Hypnodendra-ceae Broth Pterobryellaceae WRBuck amp Vitt Racopilaceae Kindb

Order Ptychomniales WRBuck CJCox AJShaw amp GoffinetPtychomniaceae MFleisch

Order Hookeriales MFleischDaltoniaceae Schimp Hookeriaceae Schimp HypopterygiaceaeMitt Leucomiaceae Broth Pilotrichaceae Kindb SaulomataceaeWRBuck CJCox AJShaw amp Goffinet Schimperobryaceae WR

17

Buck CJCox AJShaw amp GoffinetOrder Hypnales WRBuck amp Vitt

Amblystegiaceae GRoth Anomodontaceae Kindb BrachytheciaceaeSchimp Calliergonaceae Vanderpoorten Hedenaumls CJCox amp AJShaw Catagoniaceae WRBuck amp Ireland Climaciaceae KindbCryphaeaceae Schimp Echinodiaceae Broth Entodontaceae KindbFabroniaceae Schimp Fontinalaceae Schimp Helodiaceae OchyraHeterocladiaceae Ignatov amp Ignatova Hylocomiaceae MFleischHypnaceae Schimp Lembophyllaceae Broth LeptodontaceaeSchimp Lepyrodontaceae Broth Leskeaceae Schimp Leucodon-taceae Schimp Meteoriaceae Kindb Microtheciellaceae HAMillamp AJHarr Myriniaceae Schimp Myuriaceae MFleisch NeckeraceaeSchimp Orthorrhynchiaceae SHLin Phyllogoniaceae KindbPlagiotheciaceae MFleisch Pleuroziopsidaceae Ireland Prionodon-taceae Broth Pseudoleskeaceae Schimp PseudoleskeellaceaeIgnatov amp Ignatova Pterigynandraceae Schimp PterobryaceaeKindb Pylaisiaceae Schimp Pylaisiadelphaceae Goffinet amp WRBuck Regmatodontaceae Broth Rhytidiaceae Broth RigodiaceaeHACrum Rutenbergiaceae MFleisch Scorpidiaceae Ignatov ampIgnatova Sematophyllaceae Broth Sorapillaceae MFleisch Ste-reophyllaceae WRBuck amp Ireland Symphyodontaceae MFleischTheliaceae MFleisch Thuidiaceae Schimp TrachylomataceaeWRBuck amp Vitt

Acknowledgements

Sincere thanks are due to JLReveal (Ithaca) as well as WFPrudhomme van Reine and JFVeldkamp(Leiden) for comments and discussions about suprafamilial taxonomy to DQuandt (Dresden) for providingDNA from Rhacocarpus and Bartramiaceae species and to BGiesicke (Berlin) for technical assistance

References

BECKERT S H MUHLE D PRUCHNER amp V KNOOP (2001) The mitochondrial nad2 geneas a novel marker locus for phylogenetic analysis of early land plants a comparative analysis inmosses - Mol Phylogenet Evol 18 117-126

BELL NE amp AE NEWTON (2004) Systematic studies of non-hypnanaean pleurocarps establishinga phylogenetic framework for investigating the origins of pleurocarpy - In GOFFINET BV HOLLOWELL amp R MAGILL (eds) Molecular systematics of bryophytes Monogr Syst BotMissouri Bot Gard 98 290-319

BELL NE amp AE NEWTON (2007) Pleurocarpy in the Rhizogoniaceous grade - In NEWTONAE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolution SystematicsAssociation Special Volume Series 71 41-64

BELL NE D QUANDT TJ OBRIEN amp AE NEWTON (2007) Taxonomy and phylogeny inthe earliest diverging pleurocarps square holes and bifurcating pegs - Bryologist 110 533-560

BORSCH T KW HILU D QUANDT V WILDE C NEINHUIS amp W BARTHLOTT(2003) Non-coding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms- J Evol Biol 16 558-576

18

BUCK WR (2007) The history of pleurocarp classification two steps forward one step back - InNEWTON AE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 1-18

BUCK WR amp B GOFFINET (2000) Morphology and classification of mosses - In SHAWAJ amp B GOFFINET (eds) Bryophyte Biology pp 71-123 Cambridge University PressCambridge

CHIANG TY BA SCHAAL amp CI PENG (1998) Universal primers for amplification andsequencing a noncoding spacer between atpB and rbcL genes of chloroplast DNA - Bot Bull AcadSin 39 245-250

COX CJ B GOFFINET AE NEWTON AJ SHAW amp TAJ HEDDERSON (2000)Phylogenetic relationships among the diplolepideous-alternate mosses (Bryidae) inferred from nuclearand chloroplast DNA sequences - Bryologist 103 224-241

COX CJ B GOFFINET AJ SHAW amp SB BOLES (2004) Phylogenetic relationships amongthe mosses based on heterogeneous Bayesian analysis of multiple genes from multiple genomiccompartments - Syst Bot 29 234-250

CRANDALL-STOTLER B (1986) Morphogenesis developmental anatomy and bryophytephylogenetics contra-indications of monophyly - J Bryol 14 1-23

CROSBY MR RE MAGILL B ALLEN amp S HE (1999) A checklist of the mosses - MissouriBotanical Garden St Louis Missouri

DOWELD A (2001) Prosyllabus Tracheophytorum - GEOS Moscow i-lxxx + 110 pp

DOYLE JJ amp JL DOYLE (1990) Isolation of plant DNA from fresh tissue - Focus 12 13-15

DUFF RJ JC VILLAREAL DC CARGILL amp KS RENZAGLIA (2007) Progress andchallenges towards developing a phylogeny and classification of the hornworts - Bryologist 110214-243

FLEISCHER M (1920) Natuumlrliches System der Laubmoose - Hedwigia 61 390-400

FORREST LL EC DAVIS DG LONG BJ CRANDALL-STOTLER A CLARK ampML HOLLINGSWORTH (2006) Unraveling the evolutionary history of the liverworts (Marchantio-phyta) multiple taxa genomes and analyses - Bryologist 109 303-334

FRAHM J-P amp W FREY (1987) Moosflora 2 Aufl - UTB 1250 Stuttgart

FREY W (1977) Neue Vorstellungen uumlber die Verwandtschaftsgruppen und die Stammesgeschichteder Laubmoose - In FREY W H HURKA amp F OBERWINKLER (Hrsg) Beitraumlge zur Biologieder Pflanzen pp 117-139 Stuttgart

FREY W amp M STECH (2005) A morpho-molecular classification of the liverworts (Hepa-ticophytina Bryophyta) - Nova Hedwigia 81 55-78

FREY W M STECH amp K MEIszligNER (1999) Chloroplast DNA-relationship in palaeoaustralLopidium concinnum (Hypopterygiaceae Musci) An example of steno-evolution in mosses Studiesin austral temperate rain forest bryophytes 2 - Plant Syst Evol 218 67-75

GOFFINET B amp WR BUCK (2004) Systematics of Bryophyta (mosses) from molecules to arevised classification - In GOFFINET B V HOLLOWELL amp R MAGILL (eds) Molecularsystematics of bryophytes Monogr Syst Bot Missouri Bot Gard 98 205-239

GOFFINET B CJ COX AJ SHAW amp TAJ HEDDERSON (2001) The Bryophyta (mosses)Systematic and evolutionary inferences from an rps4 gene (cpDNA) phylogeny - Ann Bot 87191-208

GOFFINET B NJ WICKETT O WERNER RM ROS AJ SHAW amp CJ COX (2007)Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae(Bryophyta) - Ann Bot 99 747-753

19

GROTH-MALONEK M D PRUCHNER F GREWE amp V KNOOP (2005) Ancestors oftrans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosseswith vascular plants - Mol Biol Evol 22 117-125

HATTORI S amp H INOUE (1958) Preliminary report on Takakia lepidozioides - J Hattori BotLab 19 133-137

HE-NYGREacuteN X A JUSLEacuteN I AHONEN D GLENNY amp S PIIPPO (2006) Illuminating theevolutionary history of liverworts (Marchantiophyta) - towards a natural classification - Cladistics22 1-31

HEDDERSON TAJ DJ MURRAY CJ COX amp TL NOWELL (2004) Phylogeneticrelationships of haplolepideous mosses (Dicranidae) inferred from rps4 gene sequences - Syst Bot29 29-41

LA FARGE C BD MISHER JA WHEELER DP WALL K JOHANNES S SCHAFFERamp AJ SHAW (2000) Phylogenetic relationships within the haplolepideous mosses - Bryologist103 257-276

LA FARGE C AJ SHAW amp DH VITT (2002) The circumscription of the Dicranaceae(Bryopsida) based on the chloroplast regions trnL-trnF and rps4 - Syst Bot 27 435-452

MAGOMBO ZLK (2003) The phylogeny of basal peristomate mosses evidence from cpDNAand implications for peristome evolution - Syst Bot 28 24-38

MCNEILL J FR BARRIE HM BURDET V DEMOULIN DL HAWKSWORTHK MARHOLD DH NICOLSON J PRADO PC SILVA JE SKOG JH WIERSEMA ampNJ TURLAND (2006) International Code of Botanical Nomenclature (Vienna Code) - RegnumVegetabile 146 1-568

MUumlLLER K (2004) PRAP - computation of Bremer support for large data sets - Mol PhylogenetEvol 31 780-782

MUumlLLER K (2005) SeqState - primer design and sequence statistics for phylogenetic DNA datasets - Appl Bioinformatics 4 65-69

MUumlLLER K D QUANDT J MUumlLLER amp C NEINHUIS (2005) PhyDE v0992 PhylogeneticData Editor - httpwwwphydede

MURRAY BM (1988) Systematics of the Andreaeopsida (Bryophyta) two orders with links toTakakia - Nova Hedwigia Beih 90 289-336

NEWTON AE amp RS TANGNEY (eds) (2007) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 CRC Press Boca Raton 434 pp

NEWTON AE CJ COX JG DUCKETT JA WHEELER B GOFFINET TAJ HEDDER-SON amp BD MISHLER (2000) Evolution of the major moss lineages Phylogenetic analyses basedon multiple gene sequences and morphology - Bryologist 103 187-211

NEWTON AE N WIKSTROumlM NE BELL LL FORREST amp MS IGNATOV (2007)Dating the diversification of the pleurocarpous mosses - In NEWTON AE amp RS TANGNEY(eds) Pleurocarpous mosses systematics and evolution Systematics Association Special VolumeSeries 71 337-366

NIXON KC (1999) The parsimony ratchet a new method for rapid parsimony analysis - Cladistics15 407-411

OBRIEN TJ (2007) The phylogenetic distribution of pleurocarpous mosses evidence fromcpDNA sequences - In NEWTON AE amp RS TANGNEY (eds) Pleurocarpous mossessystematics and evolution Systematics Association Special Volume Series 71 19-41

OCHYRA R (2002) Nomenclatural changes in subfamilies of the Dicranaceae - CryptogamieBryol 23 345-349

20

OCHYRA R J ŻARNOWIEC amp H BEDNAREK-OCHYRA (2003) Census catalogue ofPolish mosses - Biodiv Poland 3 1-372

PEDERSEN N amp AE NEWTON (2007) Phylogenetic and morphological studies within thePtychomniales with emphasis on the evolution of dwarf males - In NEWTON AE amp RSTANGNEY (eds) Pleurocarpous mosses systematics and evolution Systematics AssociationSpecial Volume Series 71 367-392

QUANDT D amp M STECH (2005) Molecular evolution and secondary structure of the chloroplasttrnL intron in bryophytes - Mol Phylogenet Evol 36 429-443

QUANDT D K MUumlLLER amp S HUTTUNEN (2003) Characterisation of the chloroplast DNApsbT-H region and the influence of dyad symmetrical elements on phylogenetic reconstructions -Plant Biol 5 400-410

QUANDT D K MUumlLLER M STECH W FREY KW HILU amp T BORSCH (2004) Molecularevolution of the chloroplast trnL-F-region in land plants - In GOFFINET B V HOLLOWELL ampR MAGILL (eds) Molecular systematics of bryophytes Monogr Syst Bot Missouri Bot Gard98 13-37

QUANDT D NE BELL amp M STECH (2007) Unravelling the knot the Pulchrinodaceae famnov (Bryales) - In KUumlRSCHNER H T PFEIFFER amp M STECH (eds) A Festschrift to Wolf-gang Frey - a scientists life between deserts and rain forests Nova Hedwigia Beih 131 21-39

QIU Y-L Y CHO JC COX amp JD PALMER (1998) The gain of three mitochondrial intronsidentifies liverworts as the earliest land plants - Nature 394 671-674

QIU Y-L L LI B WANG Z CHEN V KNOOP M GROTH-MALONEK O DOM-BROVSKA J LEE L KENT J REST GF ESTABROOK TA HENDRY DW TAYLORCM TESTA M AMBROS B CRANDALL-STOTLER J DUFF M STECH W FREYD QUANDT amp CC DAVIS (2006) The deepest divergences in land plants inferred fromphylogenomic evidence - Proc Natl Acad Sci USA 103 15511-15516

RENZAGLIA KS S SCHUETTE RJ DUFF R LIGRONE AJ SHAW BD MISHLER ampJG DUCKETT (2007) Bryophyte phylogeny Advancing the molecular and morphological frontiers- Bryologist 110 179-213

SAMIGULLIN TH SP YACENTYUK GV DEGTYARYEVA KM VALIEJO-ROMANVK BOBROVA I CAPESIUS WF MARTIN AV TROITSKY VR FILIN amp ASANTONOV (2002) Paraphyly of bryophytes and close relationships of hornworts and vascularplants inferred from analysis of chloroplast rDNA ITS (cpITS) sequences - Arctoa 11 31-43

SANG T DJ CRAWFORD amp TF STUESSY (1997) Chloroplast DNA phylogeny reticulateevolution and biogeography of Paeonia (Paeoniaceae) - Amer J Bot 84 1120-1136

SHAW AJ amp KS RENZAGLIA (2004) Phylogeny and diversification of bryophytes - AmerJ Bot 91 1557-1581

SHAW AJ CJ COX amp B GOFFINET (2005) Global patterns of moss diversity taxonomic andmolecular inferences - Taxon 54 337-352

STECH M (1999a) A reclassification of Dicranaceae (Bryopsida) based on non-coding cpDNAsequence data - J Hattori Bot Lab 86 137-159

STECH M (1999b) A molecular systematic contribution to the position of Amphidium Schimp(Rhabdoweisiaceae Bryopsida) - Nova Hedwigia 68 291-300

STECH M (2004) Supraspecific circumscription and classification of Campylopus Brid(Dicranaceae Bryopsida) based on molecular data - Syst Bot 29 817-824

STECH M amp D QUANDT (2006) Molecular evolution of the chloroplast atpB-rbcL spacer inbryophytes - In SHARMA AK amp A SHARMA (eds) Plant Genome Biodiversity and EvolutionVol 2 Part B pp 409-431 Science Publishers Enfield New Hampshire

21

STECH M D QUANDT amp W FREY (2003) Molecular circumscription of the hornworts(Antho-cerotophyta) based on the chloroplast DNA trnL-trnF region - J Plant Res 116 389-398

STOTLER RE amp B CRANDALL-STOTLER (2005) A revised classification of theAnthocerotophyta and a checklist of the hornworts of North America north of Mexico - Bryologist108 16-26

SWOFFORD DL (2002) PAUP Phylogenetic analysis using parsimony (and other methods)version 40b10 - Sunderland MA

TABERLET P L GIELLY G PAUTOU amp J BOUVET (1991) Universal primers for amplificationof three non-coding regions of chloroplast DNA - Plant Mol Biol 17 1105-1109

TSUBOTA H Y AGENO B ESTEacuteBANEZ T YAMAGUCHI amp H DEGUCHI (2003)Molecular phylogeny of the Grimmiales (Musci) based on chloroplast rbcL sequences - Hikobia 1455-70

TSUBOTA H E DE LUNA D GONZAacuteLEZ MS IGNATOV amp H DEGUCHI (2004) Molecularphylogenetics and ordinal relationships based on analyses of a large-scale data set of 600 rbcLsequences of mosses - Hikobia 14 149-170

VITT DH (1984) Classification of the Bryopsida - In SCHUSTER RM (ed) New Manual ofBryology 2 696-759 Hattori Botanical Laboratory Nichinan Japan

VITT DH B GOFFINET amp T HEDDERSON (1998) 8 The ordinal classification of the mossesquestions and answers for the 1990s - In BATES JW NW ASHTON amp JG DUCKETT (eds)Bryology for the twenty-first century British Bryol Soc pp 113-123

Received 3 September 2007 accepted in revised form 30 October 2007

Page 10: botanica parcial 3

10

Consequently resolving the phylogeny of Dicranidae with confidence is one of themajor future challenges in moss systematics

As mentioned above Dicranaceae are monophyletic in a narrow circumscriptionaccording to molecular data In contrast to former Campylopoideae andParaleucobryoideae the status of Rhabdoweisioideae (= Oncophoroideae Ochyra2002) and Dicranelloideae needs further consideration Stech (1999ab) suggestedto recognise RhabdoweisioideaeRhabdoweisiaceae in a broad sense includingDicranoweisia Amphidium and Aongstroemia Subsequent molecular analysesconfirmed a close relationship of the genera Arctoa Cynodontium DicranoweisiaKiaeria Oncophorus Oreoweisia Oreas Rhabdoweisia and Symblepharis althoughwithout significant support (La Farge et al 2002 Tsubota et al 2003 Hedderson etal 2004) With respect to the molecular evidence available so far we propose toelevate Oncophoroideae to family level to accomodate these genera and perhapsGlyphomitrium (cf Tsubota et al 2003) whereas we consider AongstroemiaDichodontium and Diobelonella to belong to Aongstroemiaceae (cf Stech 1999a)Amphidium is neither closely related to Dicranaceae sstr nor to Oncophoroideae(La Farge et al 2002 Tsubota et al 2003 Hedderson et al 2004 Stech 2004 thisstudy) and should be treated at family level rather than placed in Dicranaceae assubfam Amphidioideae (Ochyra et al 2003) The circumscription of Dicranelloideaeis more difficult to evaluate as few representatives have been included in molecularanalyses However Dicranella heteromalla (Hedw) Schimp as well as the generaCampylopodium and Microcampylopus are clearly separated from Dicranaceae sstr(Stech 1999a 2004 La Farge et al 2002 Tsubota et al 2003 Hedderson et al2004) and consequently the subfamily deserves family status as well Finallymolecular data showed that the genus Hypodontium does not belong to Pottiaceae(Hedderson et al 2004 Tsubota et al 2004) Taxonomic conclusions have not beendrawn from these results which is made up here (see taxonomy)

All mosses with diplolepideous-alternate peristomes together with Splachnales witha diplolepideous-opposite (Funaria-type) peristome form a monophyletic group inmolecular analyses (eg Newton et al 2000 Beckert et al 2001 Goffinet et al2001 Cox et al 2004 Tsubota et al 2004 references in Table 2) Differentclassifications of this by far most species-rich group of mosses were proposed (egVitt et al 1998 Ochyra et al 2003 Goffinet amp Buck 2004) However at least someof the recognised subclasses and superorders are paraphyletic according to themolecular topologies and assigning formal ranks to all evolutionarily significantmonophyletic entities is problematic if the main taxonomic framework of Bryophytaand Bryopsida should be maintained (cf discussion in Bell et al 2007) Thereforein the present synopsis only one subclass Bryidae is recognised for all diplolepideous-alternate mosses and Splachnales This broadly defined Bryidae is subdivided into13 orders most of them resolved as monophyletic in the majority of the phylogeneticanalyses summarised in Table 2 although with different levels of statistical supportin maximum parsimony analyses To define monophyletic lineages at supraordinallevel informal node-based names may be chosen according to Bell et al (2007) Forexample the pleurocarpous mosses (pleurocarpy sensu Bell amp Newton 2007) andtheir closest acrocarpous relatives (Orthodontiales to Hypnales) were already

11

Table 2 Taxon sampling and bootstrap support (BS) for Dicranidae Bryidae and orders within theBryidae in recent phylogenetic analyses (MP only) based on combined molecular markers Markersare given in square brackets (non-coding regions in bold) numbers of included taxa in brackets ++respective clade present with ge 80 BS + clade present with lt 80 BS - clade not present no oronly one representative included

Bell amp Newton OBrien Quandt et al Bell et al this study(2004) (2007) (2007) (2007)

[rbcL rps4 [atpB atpB- [rbcL rps4 [rbcL rps4 [atpB-rbcLnad5] rbcL rbcL trnL-F nad5] trnL-F nad5] psbA-trnH

rps4 trnL-F] trnL]

Dicranidae + (2) + (4) ++ (3) (1) ++ (19)Bryidae ++ (57) + (53) ++ (52) ++ (98) ++ (58)Hedwigiales ++ (2) (1) ++ (2) ++ (2) - (3)Bartramiales ++ (2) ++ (4) ++ (4) ++ (3) - (4)Splachnales (0) ++ (2) ++ (3) ++ (2) ++ (5)Bryales - (4) - (5) ++ (18) + (17) - (8)Orthotrichales (1) ++ (3) ++ (3) ++ (2) ++ (4)Orthodontiales + (4) + (4) + (3) + (6) - (3)Aulacomniales + (6) + (7) ++ (2) + (7) + (3)Rhizogoniales ++ (13) + (8) ++ (5) ++ (14) - (3)Hypnodendrales ++ (13) + (7) ++ (4) ++ (29) ++ (6)Ptychomniales ++ (3) ++ (3) (1) ++ (4) (1)Hookeriales - (4) + (2) (1) + (2) + (8)Hypnales - (5) - (7) ++ (5) ++ (10) + (10)

summarised under the informal node based name pleurcarpids (Bell et al 2007)and can be distinguished from a basal grade of acrocarpous or cladocarpous lineages(Hedwigiales to Orthotrichales) Within the latter monophyly of BartramialesSplachnales and Orthotrichales is well-supported in all analyses including two ormore taxa except Bartramiales in the present data set (cf Fig 1) In contrast Bryalesreceive significant support less frequently (but see Bell et al 2007 Quandt et al2007) Hedwigiales are well supported if only Hedwigia (Hedwigiaceae) andRhacocarpus (Rhacocarpaceae) are included whereas the monospecific Helicophyllum(Helicophyllaceae) is not closely related to these taxa but shows affinities withBartramiales (Goffinet et al 2001 this study) With respect to the differentmorphologies of Helicophyllaceae and Bartramiaceae however the former shouldbe separated at ordinal level (see taxonomy)

Clarifying relationships of the Orthotrichales is still a difficult issue Analyses ofsingle chloroplast markers or parsimony analyses of combined markers from differentgenomes mostly indicated a close relationship either with Splachnales (eg Cox etal 2000 Newton et al 2000 Tsubota et al 2004 Quandt et al 2007) or with thepleurocarpids (Goffinet et al 2001 this study) Although none of these alternativesis well-supported the latter seems more likely with regard to the moderately tomaximally supported Orthotrichales - pleurocarpid sister group relationship in allanalyses of mitochondrial data and in likelihood analyses of combined plastidmitochondrial markers (Beckert et al 2001 Quandt et al 2007)

12

The molecular polyphyly of Rhizogoniaceae (eg Bell amp Newton 2004) was solvedby the transfer of rhizogonioid genera into broadly defined Aulacomniaceae andOrthodontiaceae (Bell et al 2007) which now include both acrocarpous andpleurocarpous taxa These systematic changes are also comprehensible by non-molecular characters such as morphological traits shared by Mesochaete andAulacomnium heterostichum (Hedw) Bruch amp Schimp or the variously reducedperistomes of Orthodontiaceae pp in contrast to the generally fully developed Bryum-type peristomes of rhizogonioid and hypnodendroid mosses (Bell et al 2007) Theposition of the solely pleurocarpous Hypnodendrales sister to the former Hypnidaeled to the recognition of the informal group core pleurocarps (Bell et al 2007)The former Hypnidae (Ptychomniales Hookeriales and Hypnales summarised ashomocostate pleurocarps) are monophyletic in most molecular analyses (eg Goffinetet al 2001 Tsubota et al 2004 Bell et al 2007) with Ptychomniales being well-supported (Pedersen amp Newton 2007 Table 2) Clarifying relationships betweenHookeriales and Hypnales and within the latter is still a challenge but recent molecularstudies seem to support a sister group relationship of both orders (Bell et al 2007present study)

Phylogenetic utility of non-coding plastid markers

Non-coding plastid markers that comprise both variable and conserved regionssuch as the trnL

UAA intron have repeatedly been shown to possess potential for

resolving relationships at high taxonomic levels (eg Borsch et al 2003 Quandtet al 2004) Both the trnL intron and atpB-rbcL spacer were characterised indetail in mosses with respect to their structure and molecular evolution (Quandt ampStech 2005 Stech amp Quandt 2006) They include conservative regions that can beunambiguosly aligned and even parts of the more variable regions can be used ifrepeats hairpin loops etc are correctly identified and adequately treated in thephylogenetic analyses (eg Quandt et al 2003 Quandt amp Stech 2005) Using theatpB-rbcL spacer alone (Stech amp Quandt 2006) relationships of the major mosslineages were largely consistent with the ldquototal evidencerdquo molecular tree of Goffinetamp Buck (2004) However in addition to general limitations that result from singlemarker analyses the use of non-coding markers may pose further problems suchas a high amount of homoplasy resulting in low resolution or low statistical supportfor many clades Therefore several recent molecular studies of relationships withinBryidae have employed both coding and non-coding markers (Table 2)Nevertheless the usefulness of analyses of combined non-coding plastid markerscannot be ruled out In fact Fig 1 and Table 2 indicate a phylogenetic signal inthe present data set as many clades are recovered that are usually also resolvedin analyses of coding or combined coding and non-coding markers Especiallywith regard to statistical support however the present analysis is inferior tothose of other recent data sets especially Bell et al (2007) and Quandt et al(2007) In addition the non-coding markers used here are of different suitabilityand even the two intergenic spacers differ considerably from each other ThepsbA-trnH spacer contributes much less to the trees resolution than the atpB-rbcL spacer first because it is much shorter and second because relatively largeparts are attributed to hairpin loops or otherwise hypervariable regions These

13

results indicate that future studies should evaluate the molecular evolution andphylogenetic potential of new markers both coding and con-coding and choosethe most suitable ones in a combined analysis to resolve the remaining uncertaintiesin moss phylogeny

Taxonomy

Takakiaceae Stech amp WFrey stat nov

Plantae virides nusquam rhizophorae sine protonemate e caudicis rhizomatis erectae Caudicesrhizomati et axes geotropi radiformes frequenter intercalariter ramificantes sine phyllidiis cumpapillis mucilaginis rostratis Caules phyllidiiferi saepe furcati Phyllidia sine lamina et costadistincta profunde 2-4(-5)-lobata pluristratosa tristicha sed torsione spiraliter disposita Filumcentralium in ambabus generationibus (axibus gametophyti et setis) adest Plantae dioicae Antheridiaet archegonia nuda Sporophytum terminale solitarium Seta persistens Capsula tortilis admaturitatem schizocarpa secus unam rimam spiralem longitudinalem dehiscens Stomata etoperculum absunt peristomium nullum Calyptra mitriformis

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiaceae SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval (Art 411)

Takakiales Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiales SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval

Takakiales SHatt amp Inoue ex RMSchust J Hattori Bot Lab 26 224 1963 nom inval (cumdescr latin)

Takakiopsida Stech amp WFrey statnov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiopsida Goffinet amp WRBuck Monogr Syst Bot Missouri Bot Gard 98 232 2004 nominval

Takakiopsida Jia et al Acta Phytotax Sin 41 350 351 2003 nom nud

Takakiopsida Wang amp Wu Fl Bryophyt Sin 8 447 2004 nom inval (cum descr latin)

Takakiophytina Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue JHattori Bot Lab 19 137 1958

Gigaspermidae Stech amp WFrey subclass nov

Plantae acrocarpae terrestres stoloniferae ramis brevibus erectis Folia unicostata cellulis laxislaevibus Capsula plerumque valde rugosa gymnostomatica vel cleistocarpa stomata cum duabuscellulis sociis Ab Funariidis et Encalyptidis charactere phylogenomico (71-kb inversio abest)separatae

14

TYPUS Gigaspermum Lindb Oumlfversigt af Foumlrhandlingar Kongl Svenska Vetenskaps-Akademien21 599 1865

Amphidiaceae Stech stat nov

Based on Dicranaceae subfam Amphidioideae Ochyra in Ochyra Zarnowiec amp Bednarek-OchyraCens Cat Polish Mosses 110 2003

TYPUS Amphidium Schimp Coroll Bryol Eur 39 1856

Amphidiaceae AJESm Moss Fl Britain Ireland 2nd ed 657 2004 nom inval descr angl

Dicranellaceae Stech stat nov

Based on Dicranaceae subfam Dicranelloideae Lindb Utkast Eur Bladmoss 33 1878[lsquoUnderfamilje Dicranelleaersquo]

TYPUS Dicranella (MuumlllHal) Schimp Coroll Bryol Eur 13 1856

Oncophoraceae Stech stat nov

Based on Dicranaceae subfam Oncophoroideae Lindb Utkast Eur Bladmoss 34 1878[lsquoUnderfamilje Oncophoreaersquo]

TYPUS Oncophorus (Brid) Brid Bryol Univ 1 389 1826

Hypodontiaceae Stech fam nov

Plantae robustae characteribus morphologicis Pottiaceis et Calymperaceis similes sedcharacteribus molecularicis separatae Bracteae perichaetiales internae e basi vaginantes subulataevel aristatae Capsula aspectu succulenta cellulae exothecii incrassatae annulus magnopereabsens Peristomii dentes breves triangulati incurvati aurantiaci leves vel infirme verrucosiCalyptra cucullata

TYPUS Hypodontium MuumlllHal Hedwigia 38 96 1899

Helicophyllales Stech amp WFrey ord nov

Plantae acrocarpae prostratae tomentosae Folia dimorpha in duas series laterales et unam seriemventralem divisa Costa percurrens Cellulae hexagonae ad subquadratae papillosae Capsula immersacupulata ad oblonga infra orificium abrupte incurvata stomata destituta Peristomium nullum Sporaeisomorphae heteropolares granulatae

TYPUS Helicophyllum Brid Bryol Univ 2 771 1827

Synopsis of the suprageneric classification of BryophytaAuthor citations are in accordance with Art 492 of the Vienna Code (McNeill et al 2006)

Subdivision Takakiophytina Stech amp WFreyClass Takakiopsida Stech amp WFrey

Order Takakiales Stech amp WFreyTakakiaceae Stech amp WFrey

Subdivision Sphagnophytina DoweldClass Sphagnopsida Schimp

Order Sphagnales Limpr

15

Sphagnaceae DumortOrder Ambuchananiales Seppelt amp HACrum

Ambuchananiaceae Seppelt amp HACrumSubdivision Bryophytina Engler

Class Andreaeopsida JHSchaffnSubclass Andreaeidae Engl

Order Andreaeales LimprAndreaeaceae Dumort

Subclass Andreaeobryidae OchyraOrder Andreaeobryales BMMurray

Andreaeobryaceae Steere amp BMMurrayClass Oedipodiopsida Goffinet amp WRBuck

Order Oedipodiales Goffinet amp WRBuckOedipodiaceae Schimp

Class Tetraphidopsida Goffinet amp WRBuckOrder Tetraphidales MFleisch

Tetraphidaceae SchimpClass Polytrichopsida Doweld

Order Polytrichales MFleischPolytrichaceae Schwaumlgr

Class Bryopsida PaxSubclass Buxbaumiidae Doweld

Order Buxbaumiales MFleischBuxbaumiaceae Schimp

Subclass Diphysciidae OchyraOrder Diphysciales MFleisch

Diphysciaceae MFleischSubclass Timmiidae Ochyra

Order Timmiales OchyraTimmiaceae Schimp

Subclass Encalyptidae Ochyra Żarnowiec amp Bednarek-OchyraOrder Encalyptales Dixon

Encalyptaceae SchimpSubclass Funariidae Ochyra

Order Funariales MFleischFunariaceae Schwaumlgr Disceliaceae Schimp

Subclass Gigaspermidae Stech amp WFreyOrder Gigaspermales Goffinet Wickett OWerner Ros AJShaw amp CJCox

Gigaspermaceae LindbSubclass Dicranidae Doweld

Order Catoscopiales Ignatov amp IgnatovaCatoscopiaceae Broth

Order Scouleriales Goffinet amp WRBuckDrummondiaceae Goffinet Scouleriaceae SPChurchill

Order Bryoxiphiales HACrum amp LEAndersonBryoxiphiaceae Besch

16

Order Grimmiales MFleischGrimmiaceae Arn Ptychomitriaceae Schimp Seligeriaceae Schimp

Order Archidiales LimprArchidiaceae Schimp

Order Mitteniales ShawMitteniaceae Broth

Order Dicranales HPhilib ex MFleischAmphidiaceae Stech Aongstroemiaceae De Not BruchiaceaeSchimp Calymperaceae Kindb Dicranaceae Schimp Dicranel-laceae Stech Ditrichaceae Limpr Erpodiaceae Broth EustichiaceaeBroth Fissidentaceae Schimp Leucobryaceae Schimp Onco-phoraceae Stech Rhachitheciaceae HRob Schistostegaceae SchimpViridivelleraceae IGStone Wardiaceae Welch

Order Pottiales MFleischEphemeraceae Schimp Hypodontiaceae Stech PleurophascaceaeBroth Pottiaceae Schimp Serpotortellaceae WDReese amp RHZander

Subclass Bryidae EnglOrder Hedwigiales Ochyra

Hedwigiaceae Schimp Rhacocarpaceae KindbOrder Helicophyllales Stech amp WFrey

Helicophyllaceae BrothOrder Bartramiales DQuandt NEBell amp Stech

Bartramiaceae SchwaumlgrOrder Splachnales Ochyra

Meesiaceae Schimp Splachnaceae Grev amp ArnOrder Bryales Limpr

Bryaceae Schwaumlgr Leptostomataceae Schwaumlgr Mniaceae SchwaumlgrPhyllodrepaniaceae Crosby Pseudoditrichaceae Steere amp ZIwatsPulchrinodaceae DQuandt NEBell amp Stech

Order Orthotrichales DixonOrthotrichaceae Arn

Order Orthodontiales NEBell AENewton amp DQuandtOrthodontiaceae Goffinet

Order Aulacomniales NEBell AENewton amp DQuandtAulacomniaceae Schimp

Order Rhizogoniales Goffinet amp WRBuckRhizogoniaceae Broth

Order Hypnodendrales NEBell AENewton amp DQuandtBraithwaiteaceae NEBell AENewton amp DQuandt Hypnodendra-ceae Broth Pterobryellaceae WRBuck amp Vitt Racopilaceae Kindb

Order Ptychomniales WRBuck CJCox AJShaw amp GoffinetPtychomniaceae MFleisch

Order Hookeriales MFleischDaltoniaceae Schimp Hookeriaceae Schimp HypopterygiaceaeMitt Leucomiaceae Broth Pilotrichaceae Kindb SaulomataceaeWRBuck CJCox AJShaw amp Goffinet Schimperobryaceae WR

17

Buck CJCox AJShaw amp GoffinetOrder Hypnales WRBuck amp Vitt

Amblystegiaceae GRoth Anomodontaceae Kindb BrachytheciaceaeSchimp Calliergonaceae Vanderpoorten Hedenaumls CJCox amp AJShaw Catagoniaceae WRBuck amp Ireland Climaciaceae KindbCryphaeaceae Schimp Echinodiaceae Broth Entodontaceae KindbFabroniaceae Schimp Fontinalaceae Schimp Helodiaceae OchyraHeterocladiaceae Ignatov amp Ignatova Hylocomiaceae MFleischHypnaceae Schimp Lembophyllaceae Broth LeptodontaceaeSchimp Lepyrodontaceae Broth Leskeaceae Schimp Leucodon-taceae Schimp Meteoriaceae Kindb Microtheciellaceae HAMillamp AJHarr Myriniaceae Schimp Myuriaceae MFleisch NeckeraceaeSchimp Orthorrhynchiaceae SHLin Phyllogoniaceae KindbPlagiotheciaceae MFleisch Pleuroziopsidaceae Ireland Prionodon-taceae Broth Pseudoleskeaceae Schimp PseudoleskeellaceaeIgnatov amp Ignatova Pterigynandraceae Schimp PterobryaceaeKindb Pylaisiaceae Schimp Pylaisiadelphaceae Goffinet amp WRBuck Regmatodontaceae Broth Rhytidiaceae Broth RigodiaceaeHACrum Rutenbergiaceae MFleisch Scorpidiaceae Ignatov ampIgnatova Sematophyllaceae Broth Sorapillaceae MFleisch Ste-reophyllaceae WRBuck amp Ireland Symphyodontaceae MFleischTheliaceae MFleisch Thuidiaceae Schimp TrachylomataceaeWRBuck amp Vitt

Acknowledgements

Sincere thanks are due to JLReveal (Ithaca) as well as WFPrudhomme van Reine and JFVeldkamp(Leiden) for comments and discussions about suprafamilial taxonomy to DQuandt (Dresden) for providingDNA from Rhacocarpus and Bartramiaceae species and to BGiesicke (Berlin) for technical assistance

References

BECKERT S H MUHLE D PRUCHNER amp V KNOOP (2001) The mitochondrial nad2 geneas a novel marker locus for phylogenetic analysis of early land plants a comparative analysis inmosses - Mol Phylogenet Evol 18 117-126

BELL NE amp AE NEWTON (2004) Systematic studies of non-hypnanaean pleurocarps establishinga phylogenetic framework for investigating the origins of pleurocarpy - In GOFFINET BV HOLLOWELL amp R MAGILL (eds) Molecular systematics of bryophytes Monogr Syst BotMissouri Bot Gard 98 290-319

BELL NE amp AE NEWTON (2007) Pleurocarpy in the Rhizogoniaceous grade - In NEWTONAE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolution SystematicsAssociation Special Volume Series 71 41-64

BELL NE D QUANDT TJ OBRIEN amp AE NEWTON (2007) Taxonomy and phylogeny inthe earliest diverging pleurocarps square holes and bifurcating pegs - Bryologist 110 533-560

BORSCH T KW HILU D QUANDT V WILDE C NEINHUIS amp W BARTHLOTT(2003) Non-coding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms- J Evol Biol 16 558-576

18

BUCK WR (2007) The history of pleurocarp classification two steps forward one step back - InNEWTON AE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 1-18

BUCK WR amp B GOFFINET (2000) Morphology and classification of mosses - In SHAWAJ amp B GOFFINET (eds) Bryophyte Biology pp 71-123 Cambridge University PressCambridge

CHIANG TY BA SCHAAL amp CI PENG (1998) Universal primers for amplification andsequencing a noncoding spacer between atpB and rbcL genes of chloroplast DNA - Bot Bull AcadSin 39 245-250

COX CJ B GOFFINET AE NEWTON AJ SHAW amp TAJ HEDDERSON (2000)Phylogenetic relationships among the diplolepideous-alternate mosses (Bryidae) inferred from nuclearand chloroplast DNA sequences - Bryologist 103 224-241

COX CJ B GOFFINET AJ SHAW amp SB BOLES (2004) Phylogenetic relationships amongthe mosses based on heterogeneous Bayesian analysis of multiple genes from multiple genomiccompartments - Syst Bot 29 234-250

CRANDALL-STOTLER B (1986) Morphogenesis developmental anatomy and bryophytephylogenetics contra-indications of monophyly - J Bryol 14 1-23

CROSBY MR RE MAGILL B ALLEN amp S HE (1999) A checklist of the mosses - MissouriBotanical Garden St Louis Missouri

DOWELD A (2001) Prosyllabus Tracheophytorum - GEOS Moscow i-lxxx + 110 pp

DOYLE JJ amp JL DOYLE (1990) Isolation of plant DNA from fresh tissue - Focus 12 13-15

DUFF RJ JC VILLAREAL DC CARGILL amp KS RENZAGLIA (2007) Progress andchallenges towards developing a phylogeny and classification of the hornworts - Bryologist 110214-243

FLEISCHER M (1920) Natuumlrliches System der Laubmoose - Hedwigia 61 390-400

FORREST LL EC DAVIS DG LONG BJ CRANDALL-STOTLER A CLARK ampML HOLLINGSWORTH (2006) Unraveling the evolutionary history of the liverworts (Marchantio-phyta) multiple taxa genomes and analyses - Bryologist 109 303-334

FRAHM J-P amp W FREY (1987) Moosflora 2 Aufl - UTB 1250 Stuttgart

FREY W (1977) Neue Vorstellungen uumlber die Verwandtschaftsgruppen und die Stammesgeschichteder Laubmoose - In FREY W H HURKA amp F OBERWINKLER (Hrsg) Beitraumlge zur Biologieder Pflanzen pp 117-139 Stuttgart

FREY W amp M STECH (2005) A morpho-molecular classification of the liverworts (Hepa-ticophytina Bryophyta) - Nova Hedwigia 81 55-78

FREY W M STECH amp K MEIszligNER (1999) Chloroplast DNA-relationship in palaeoaustralLopidium concinnum (Hypopterygiaceae Musci) An example of steno-evolution in mosses Studiesin austral temperate rain forest bryophytes 2 - Plant Syst Evol 218 67-75

GOFFINET B amp WR BUCK (2004) Systematics of Bryophyta (mosses) from molecules to arevised classification - In GOFFINET B V HOLLOWELL amp R MAGILL (eds) Molecularsystematics of bryophytes Monogr Syst Bot Missouri Bot Gard 98 205-239

GOFFINET B CJ COX AJ SHAW amp TAJ HEDDERSON (2001) The Bryophyta (mosses)Systematic and evolutionary inferences from an rps4 gene (cpDNA) phylogeny - Ann Bot 87191-208

GOFFINET B NJ WICKETT O WERNER RM ROS AJ SHAW amp CJ COX (2007)Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae(Bryophyta) - Ann Bot 99 747-753

19

GROTH-MALONEK M D PRUCHNER F GREWE amp V KNOOP (2005) Ancestors oftrans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosseswith vascular plants - Mol Biol Evol 22 117-125

HATTORI S amp H INOUE (1958) Preliminary report on Takakia lepidozioides - J Hattori BotLab 19 133-137

HE-NYGREacuteN X A JUSLEacuteN I AHONEN D GLENNY amp S PIIPPO (2006) Illuminating theevolutionary history of liverworts (Marchantiophyta) - towards a natural classification - Cladistics22 1-31

HEDDERSON TAJ DJ MURRAY CJ COX amp TL NOWELL (2004) Phylogeneticrelationships of haplolepideous mosses (Dicranidae) inferred from rps4 gene sequences - Syst Bot29 29-41

LA FARGE C BD MISHER JA WHEELER DP WALL K JOHANNES S SCHAFFERamp AJ SHAW (2000) Phylogenetic relationships within the haplolepideous mosses - Bryologist103 257-276

LA FARGE C AJ SHAW amp DH VITT (2002) The circumscription of the Dicranaceae(Bryopsida) based on the chloroplast regions trnL-trnF and rps4 - Syst Bot 27 435-452

MAGOMBO ZLK (2003) The phylogeny of basal peristomate mosses evidence from cpDNAand implications for peristome evolution - Syst Bot 28 24-38

MCNEILL J FR BARRIE HM BURDET V DEMOULIN DL HAWKSWORTHK MARHOLD DH NICOLSON J PRADO PC SILVA JE SKOG JH WIERSEMA ampNJ TURLAND (2006) International Code of Botanical Nomenclature (Vienna Code) - RegnumVegetabile 146 1-568

MUumlLLER K (2004) PRAP - computation of Bremer support for large data sets - Mol PhylogenetEvol 31 780-782

MUumlLLER K (2005) SeqState - primer design and sequence statistics for phylogenetic DNA datasets - Appl Bioinformatics 4 65-69

MUumlLLER K D QUANDT J MUumlLLER amp C NEINHUIS (2005) PhyDE v0992 PhylogeneticData Editor - httpwwwphydede

MURRAY BM (1988) Systematics of the Andreaeopsida (Bryophyta) two orders with links toTakakia - Nova Hedwigia Beih 90 289-336

NEWTON AE amp RS TANGNEY (eds) (2007) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 CRC Press Boca Raton 434 pp

NEWTON AE CJ COX JG DUCKETT JA WHEELER B GOFFINET TAJ HEDDER-SON amp BD MISHLER (2000) Evolution of the major moss lineages Phylogenetic analyses basedon multiple gene sequences and morphology - Bryologist 103 187-211

NEWTON AE N WIKSTROumlM NE BELL LL FORREST amp MS IGNATOV (2007)Dating the diversification of the pleurocarpous mosses - In NEWTON AE amp RS TANGNEY(eds) Pleurocarpous mosses systematics and evolution Systematics Association Special VolumeSeries 71 337-366

NIXON KC (1999) The parsimony ratchet a new method for rapid parsimony analysis - Cladistics15 407-411

OBRIEN TJ (2007) The phylogenetic distribution of pleurocarpous mosses evidence fromcpDNA sequences - In NEWTON AE amp RS TANGNEY (eds) Pleurocarpous mossessystematics and evolution Systematics Association Special Volume Series 71 19-41

OCHYRA R (2002) Nomenclatural changes in subfamilies of the Dicranaceae - CryptogamieBryol 23 345-349

20

OCHYRA R J ŻARNOWIEC amp H BEDNAREK-OCHYRA (2003) Census catalogue ofPolish mosses - Biodiv Poland 3 1-372

PEDERSEN N amp AE NEWTON (2007) Phylogenetic and morphological studies within thePtychomniales with emphasis on the evolution of dwarf males - In NEWTON AE amp RSTANGNEY (eds) Pleurocarpous mosses systematics and evolution Systematics AssociationSpecial Volume Series 71 367-392

QUANDT D amp M STECH (2005) Molecular evolution and secondary structure of the chloroplasttrnL intron in bryophytes - Mol Phylogenet Evol 36 429-443

QUANDT D K MUumlLLER amp S HUTTUNEN (2003) Characterisation of the chloroplast DNApsbT-H region and the influence of dyad symmetrical elements on phylogenetic reconstructions -Plant Biol 5 400-410

QUANDT D K MUumlLLER M STECH W FREY KW HILU amp T BORSCH (2004) Molecularevolution of the chloroplast trnL-F-region in land plants - In GOFFINET B V HOLLOWELL ampR MAGILL (eds) Molecular systematics of bryophytes Monogr Syst Bot Missouri Bot Gard98 13-37

QUANDT D NE BELL amp M STECH (2007) Unravelling the knot the Pulchrinodaceae famnov (Bryales) - In KUumlRSCHNER H T PFEIFFER amp M STECH (eds) A Festschrift to Wolf-gang Frey - a scientists life between deserts and rain forests Nova Hedwigia Beih 131 21-39

QIU Y-L Y CHO JC COX amp JD PALMER (1998) The gain of three mitochondrial intronsidentifies liverworts as the earliest land plants - Nature 394 671-674

QIU Y-L L LI B WANG Z CHEN V KNOOP M GROTH-MALONEK O DOM-BROVSKA J LEE L KENT J REST GF ESTABROOK TA HENDRY DW TAYLORCM TESTA M AMBROS B CRANDALL-STOTLER J DUFF M STECH W FREYD QUANDT amp CC DAVIS (2006) The deepest divergences in land plants inferred fromphylogenomic evidence - Proc Natl Acad Sci USA 103 15511-15516

RENZAGLIA KS S SCHUETTE RJ DUFF R LIGRONE AJ SHAW BD MISHLER ampJG DUCKETT (2007) Bryophyte phylogeny Advancing the molecular and morphological frontiers- Bryologist 110 179-213

SAMIGULLIN TH SP YACENTYUK GV DEGTYARYEVA KM VALIEJO-ROMANVK BOBROVA I CAPESIUS WF MARTIN AV TROITSKY VR FILIN amp ASANTONOV (2002) Paraphyly of bryophytes and close relationships of hornworts and vascularplants inferred from analysis of chloroplast rDNA ITS (cpITS) sequences - Arctoa 11 31-43

SANG T DJ CRAWFORD amp TF STUESSY (1997) Chloroplast DNA phylogeny reticulateevolution and biogeography of Paeonia (Paeoniaceae) - Amer J Bot 84 1120-1136

SHAW AJ amp KS RENZAGLIA (2004) Phylogeny and diversification of bryophytes - AmerJ Bot 91 1557-1581

SHAW AJ CJ COX amp B GOFFINET (2005) Global patterns of moss diversity taxonomic andmolecular inferences - Taxon 54 337-352

STECH M (1999a) A reclassification of Dicranaceae (Bryopsida) based on non-coding cpDNAsequence data - J Hattori Bot Lab 86 137-159

STECH M (1999b) A molecular systematic contribution to the position of Amphidium Schimp(Rhabdoweisiaceae Bryopsida) - Nova Hedwigia 68 291-300

STECH M (2004) Supraspecific circumscription and classification of Campylopus Brid(Dicranaceae Bryopsida) based on molecular data - Syst Bot 29 817-824

STECH M amp D QUANDT (2006) Molecular evolution of the chloroplast atpB-rbcL spacer inbryophytes - In SHARMA AK amp A SHARMA (eds) Plant Genome Biodiversity and EvolutionVol 2 Part B pp 409-431 Science Publishers Enfield New Hampshire

21

STECH M D QUANDT amp W FREY (2003) Molecular circumscription of the hornworts(Antho-cerotophyta) based on the chloroplast DNA trnL-trnF region - J Plant Res 116 389-398

STOTLER RE amp B CRANDALL-STOTLER (2005) A revised classification of theAnthocerotophyta and a checklist of the hornworts of North America north of Mexico - Bryologist108 16-26

SWOFFORD DL (2002) PAUP Phylogenetic analysis using parsimony (and other methods)version 40b10 - Sunderland MA

TABERLET P L GIELLY G PAUTOU amp J BOUVET (1991) Universal primers for amplificationof three non-coding regions of chloroplast DNA - Plant Mol Biol 17 1105-1109

TSUBOTA H Y AGENO B ESTEacuteBANEZ T YAMAGUCHI amp H DEGUCHI (2003)Molecular phylogeny of the Grimmiales (Musci) based on chloroplast rbcL sequences - Hikobia 1455-70

TSUBOTA H E DE LUNA D GONZAacuteLEZ MS IGNATOV amp H DEGUCHI (2004) Molecularphylogenetics and ordinal relationships based on analyses of a large-scale data set of 600 rbcLsequences of mosses - Hikobia 14 149-170

VITT DH (1984) Classification of the Bryopsida - In SCHUSTER RM (ed) New Manual ofBryology 2 696-759 Hattori Botanical Laboratory Nichinan Japan

VITT DH B GOFFINET amp T HEDDERSON (1998) 8 The ordinal classification of the mossesquestions and answers for the 1990s - In BATES JW NW ASHTON amp JG DUCKETT (eds)Bryology for the twenty-first century British Bryol Soc pp 113-123

Received 3 September 2007 accepted in revised form 30 October 2007

Page 11: botanica parcial 3

11

Table 2 Taxon sampling and bootstrap support (BS) for Dicranidae Bryidae and orders within theBryidae in recent phylogenetic analyses (MP only) based on combined molecular markers Markersare given in square brackets (non-coding regions in bold) numbers of included taxa in brackets ++respective clade present with ge 80 BS + clade present with lt 80 BS - clade not present no oronly one representative included

Bell amp Newton OBrien Quandt et al Bell et al this study(2004) (2007) (2007) (2007)

[rbcL rps4 [atpB atpB- [rbcL rps4 [rbcL rps4 [atpB-rbcLnad5] rbcL rbcL trnL-F nad5] trnL-F nad5] psbA-trnH

rps4 trnL-F] trnL]

Dicranidae + (2) + (4) ++ (3) (1) ++ (19)Bryidae ++ (57) + (53) ++ (52) ++ (98) ++ (58)Hedwigiales ++ (2) (1) ++ (2) ++ (2) - (3)Bartramiales ++ (2) ++ (4) ++ (4) ++ (3) - (4)Splachnales (0) ++ (2) ++ (3) ++ (2) ++ (5)Bryales - (4) - (5) ++ (18) + (17) - (8)Orthotrichales (1) ++ (3) ++ (3) ++ (2) ++ (4)Orthodontiales + (4) + (4) + (3) + (6) - (3)Aulacomniales + (6) + (7) ++ (2) + (7) + (3)Rhizogoniales ++ (13) + (8) ++ (5) ++ (14) - (3)Hypnodendrales ++ (13) + (7) ++ (4) ++ (29) ++ (6)Ptychomniales ++ (3) ++ (3) (1) ++ (4) (1)Hookeriales - (4) + (2) (1) + (2) + (8)Hypnales - (5) - (7) ++ (5) ++ (10) + (10)

summarised under the informal node based name pleurcarpids (Bell et al 2007)and can be distinguished from a basal grade of acrocarpous or cladocarpous lineages(Hedwigiales to Orthotrichales) Within the latter monophyly of BartramialesSplachnales and Orthotrichales is well-supported in all analyses including two ormore taxa except Bartramiales in the present data set (cf Fig 1) In contrast Bryalesreceive significant support less frequently (but see Bell et al 2007 Quandt et al2007) Hedwigiales are well supported if only Hedwigia (Hedwigiaceae) andRhacocarpus (Rhacocarpaceae) are included whereas the monospecific Helicophyllum(Helicophyllaceae) is not closely related to these taxa but shows affinities withBartramiales (Goffinet et al 2001 this study) With respect to the differentmorphologies of Helicophyllaceae and Bartramiaceae however the former shouldbe separated at ordinal level (see taxonomy)

Clarifying relationships of the Orthotrichales is still a difficult issue Analyses ofsingle chloroplast markers or parsimony analyses of combined markers from differentgenomes mostly indicated a close relationship either with Splachnales (eg Cox etal 2000 Newton et al 2000 Tsubota et al 2004 Quandt et al 2007) or with thepleurocarpids (Goffinet et al 2001 this study) Although none of these alternativesis well-supported the latter seems more likely with regard to the moderately tomaximally supported Orthotrichales - pleurocarpid sister group relationship in allanalyses of mitochondrial data and in likelihood analyses of combined plastidmitochondrial markers (Beckert et al 2001 Quandt et al 2007)

12

The molecular polyphyly of Rhizogoniaceae (eg Bell amp Newton 2004) was solvedby the transfer of rhizogonioid genera into broadly defined Aulacomniaceae andOrthodontiaceae (Bell et al 2007) which now include both acrocarpous andpleurocarpous taxa These systematic changes are also comprehensible by non-molecular characters such as morphological traits shared by Mesochaete andAulacomnium heterostichum (Hedw) Bruch amp Schimp or the variously reducedperistomes of Orthodontiaceae pp in contrast to the generally fully developed Bryum-type peristomes of rhizogonioid and hypnodendroid mosses (Bell et al 2007) Theposition of the solely pleurocarpous Hypnodendrales sister to the former Hypnidaeled to the recognition of the informal group core pleurocarps (Bell et al 2007)The former Hypnidae (Ptychomniales Hookeriales and Hypnales summarised ashomocostate pleurocarps) are monophyletic in most molecular analyses (eg Goffinetet al 2001 Tsubota et al 2004 Bell et al 2007) with Ptychomniales being well-supported (Pedersen amp Newton 2007 Table 2) Clarifying relationships betweenHookeriales and Hypnales and within the latter is still a challenge but recent molecularstudies seem to support a sister group relationship of both orders (Bell et al 2007present study)

Phylogenetic utility of non-coding plastid markers

Non-coding plastid markers that comprise both variable and conserved regionssuch as the trnL

UAA intron have repeatedly been shown to possess potential for

resolving relationships at high taxonomic levels (eg Borsch et al 2003 Quandtet al 2004) Both the trnL intron and atpB-rbcL spacer were characterised indetail in mosses with respect to their structure and molecular evolution (Quandt ampStech 2005 Stech amp Quandt 2006) They include conservative regions that can beunambiguosly aligned and even parts of the more variable regions can be used ifrepeats hairpin loops etc are correctly identified and adequately treated in thephylogenetic analyses (eg Quandt et al 2003 Quandt amp Stech 2005) Using theatpB-rbcL spacer alone (Stech amp Quandt 2006) relationships of the major mosslineages were largely consistent with the ldquototal evidencerdquo molecular tree of Goffinetamp Buck (2004) However in addition to general limitations that result from singlemarker analyses the use of non-coding markers may pose further problems suchas a high amount of homoplasy resulting in low resolution or low statistical supportfor many clades Therefore several recent molecular studies of relationships withinBryidae have employed both coding and non-coding markers (Table 2)Nevertheless the usefulness of analyses of combined non-coding plastid markerscannot be ruled out In fact Fig 1 and Table 2 indicate a phylogenetic signal inthe present data set as many clades are recovered that are usually also resolvedin analyses of coding or combined coding and non-coding markers Especiallywith regard to statistical support however the present analysis is inferior tothose of other recent data sets especially Bell et al (2007) and Quandt et al(2007) In addition the non-coding markers used here are of different suitabilityand even the two intergenic spacers differ considerably from each other ThepsbA-trnH spacer contributes much less to the trees resolution than the atpB-rbcL spacer first because it is much shorter and second because relatively largeparts are attributed to hairpin loops or otherwise hypervariable regions These

13

results indicate that future studies should evaluate the molecular evolution andphylogenetic potential of new markers both coding and con-coding and choosethe most suitable ones in a combined analysis to resolve the remaining uncertaintiesin moss phylogeny

Taxonomy

Takakiaceae Stech amp WFrey stat nov

Plantae virides nusquam rhizophorae sine protonemate e caudicis rhizomatis erectae Caudicesrhizomati et axes geotropi radiformes frequenter intercalariter ramificantes sine phyllidiis cumpapillis mucilaginis rostratis Caules phyllidiiferi saepe furcati Phyllidia sine lamina et costadistincta profunde 2-4(-5)-lobata pluristratosa tristicha sed torsione spiraliter disposita Filumcentralium in ambabus generationibus (axibus gametophyti et setis) adest Plantae dioicae Antheridiaet archegonia nuda Sporophytum terminale solitarium Seta persistens Capsula tortilis admaturitatem schizocarpa secus unam rimam spiralem longitudinalem dehiscens Stomata etoperculum absunt peristomium nullum Calyptra mitriformis

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiaceae SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval (Art 411)

Takakiales Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiales SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval

Takakiales SHatt amp Inoue ex RMSchust J Hattori Bot Lab 26 224 1963 nom inval (cumdescr latin)

Takakiopsida Stech amp WFrey statnov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiopsida Goffinet amp WRBuck Monogr Syst Bot Missouri Bot Gard 98 232 2004 nominval

Takakiopsida Jia et al Acta Phytotax Sin 41 350 351 2003 nom nud

Takakiopsida Wang amp Wu Fl Bryophyt Sin 8 447 2004 nom inval (cum descr latin)

Takakiophytina Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue JHattori Bot Lab 19 137 1958

Gigaspermidae Stech amp WFrey subclass nov

Plantae acrocarpae terrestres stoloniferae ramis brevibus erectis Folia unicostata cellulis laxislaevibus Capsula plerumque valde rugosa gymnostomatica vel cleistocarpa stomata cum duabuscellulis sociis Ab Funariidis et Encalyptidis charactere phylogenomico (71-kb inversio abest)separatae

14

TYPUS Gigaspermum Lindb Oumlfversigt af Foumlrhandlingar Kongl Svenska Vetenskaps-Akademien21 599 1865

Amphidiaceae Stech stat nov

Based on Dicranaceae subfam Amphidioideae Ochyra in Ochyra Zarnowiec amp Bednarek-OchyraCens Cat Polish Mosses 110 2003

TYPUS Amphidium Schimp Coroll Bryol Eur 39 1856

Amphidiaceae AJESm Moss Fl Britain Ireland 2nd ed 657 2004 nom inval descr angl

Dicranellaceae Stech stat nov

Based on Dicranaceae subfam Dicranelloideae Lindb Utkast Eur Bladmoss 33 1878[lsquoUnderfamilje Dicranelleaersquo]

TYPUS Dicranella (MuumlllHal) Schimp Coroll Bryol Eur 13 1856

Oncophoraceae Stech stat nov

Based on Dicranaceae subfam Oncophoroideae Lindb Utkast Eur Bladmoss 34 1878[lsquoUnderfamilje Oncophoreaersquo]

TYPUS Oncophorus (Brid) Brid Bryol Univ 1 389 1826

Hypodontiaceae Stech fam nov

Plantae robustae characteribus morphologicis Pottiaceis et Calymperaceis similes sedcharacteribus molecularicis separatae Bracteae perichaetiales internae e basi vaginantes subulataevel aristatae Capsula aspectu succulenta cellulae exothecii incrassatae annulus magnopereabsens Peristomii dentes breves triangulati incurvati aurantiaci leves vel infirme verrucosiCalyptra cucullata

TYPUS Hypodontium MuumlllHal Hedwigia 38 96 1899

Helicophyllales Stech amp WFrey ord nov

Plantae acrocarpae prostratae tomentosae Folia dimorpha in duas series laterales et unam seriemventralem divisa Costa percurrens Cellulae hexagonae ad subquadratae papillosae Capsula immersacupulata ad oblonga infra orificium abrupte incurvata stomata destituta Peristomium nullum Sporaeisomorphae heteropolares granulatae

TYPUS Helicophyllum Brid Bryol Univ 2 771 1827

Synopsis of the suprageneric classification of BryophytaAuthor citations are in accordance with Art 492 of the Vienna Code (McNeill et al 2006)

Subdivision Takakiophytina Stech amp WFreyClass Takakiopsida Stech amp WFrey

Order Takakiales Stech amp WFreyTakakiaceae Stech amp WFrey

Subdivision Sphagnophytina DoweldClass Sphagnopsida Schimp

Order Sphagnales Limpr

15

Sphagnaceae DumortOrder Ambuchananiales Seppelt amp HACrum

Ambuchananiaceae Seppelt amp HACrumSubdivision Bryophytina Engler

Class Andreaeopsida JHSchaffnSubclass Andreaeidae Engl

Order Andreaeales LimprAndreaeaceae Dumort

Subclass Andreaeobryidae OchyraOrder Andreaeobryales BMMurray

Andreaeobryaceae Steere amp BMMurrayClass Oedipodiopsida Goffinet amp WRBuck

Order Oedipodiales Goffinet amp WRBuckOedipodiaceae Schimp

Class Tetraphidopsida Goffinet amp WRBuckOrder Tetraphidales MFleisch

Tetraphidaceae SchimpClass Polytrichopsida Doweld

Order Polytrichales MFleischPolytrichaceae Schwaumlgr

Class Bryopsida PaxSubclass Buxbaumiidae Doweld

Order Buxbaumiales MFleischBuxbaumiaceae Schimp

Subclass Diphysciidae OchyraOrder Diphysciales MFleisch

Diphysciaceae MFleischSubclass Timmiidae Ochyra

Order Timmiales OchyraTimmiaceae Schimp

Subclass Encalyptidae Ochyra Żarnowiec amp Bednarek-OchyraOrder Encalyptales Dixon

Encalyptaceae SchimpSubclass Funariidae Ochyra

Order Funariales MFleischFunariaceae Schwaumlgr Disceliaceae Schimp

Subclass Gigaspermidae Stech amp WFreyOrder Gigaspermales Goffinet Wickett OWerner Ros AJShaw amp CJCox

Gigaspermaceae LindbSubclass Dicranidae Doweld

Order Catoscopiales Ignatov amp IgnatovaCatoscopiaceae Broth

Order Scouleriales Goffinet amp WRBuckDrummondiaceae Goffinet Scouleriaceae SPChurchill

Order Bryoxiphiales HACrum amp LEAndersonBryoxiphiaceae Besch

16

Order Grimmiales MFleischGrimmiaceae Arn Ptychomitriaceae Schimp Seligeriaceae Schimp

Order Archidiales LimprArchidiaceae Schimp

Order Mitteniales ShawMitteniaceae Broth

Order Dicranales HPhilib ex MFleischAmphidiaceae Stech Aongstroemiaceae De Not BruchiaceaeSchimp Calymperaceae Kindb Dicranaceae Schimp Dicranel-laceae Stech Ditrichaceae Limpr Erpodiaceae Broth EustichiaceaeBroth Fissidentaceae Schimp Leucobryaceae Schimp Onco-phoraceae Stech Rhachitheciaceae HRob Schistostegaceae SchimpViridivelleraceae IGStone Wardiaceae Welch

Order Pottiales MFleischEphemeraceae Schimp Hypodontiaceae Stech PleurophascaceaeBroth Pottiaceae Schimp Serpotortellaceae WDReese amp RHZander

Subclass Bryidae EnglOrder Hedwigiales Ochyra

Hedwigiaceae Schimp Rhacocarpaceae KindbOrder Helicophyllales Stech amp WFrey

Helicophyllaceae BrothOrder Bartramiales DQuandt NEBell amp Stech

Bartramiaceae SchwaumlgrOrder Splachnales Ochyra

Meesiaceae Schimp Splachnaceae Grev amp ArnOrder Bryales Limpr

Bryaceae Schwaumlgr Leptostomataceae Schwaumlgr Mniaceae SchwaumlgrPhyllodrepaniaceae Crosby Pseudoditrichaceae Steere amp ZIwatsPulchrinodaceae DQuandt NEBell amp Stech

Order Orthotrichales DixonOrthotrichaceae Arn

Order Orthodontiales NEBell AENewton amp DQuandtOrthodontiaceae Goffinet

Order Aulacomniales NEBell AENewton amp DQuandtAulacomniaceae Schimp

Order Rhizogoniales Goffinet amp WRBuckRhizogoniaceae Broth

Order Hypnodendrales NEBell AENewton amp DQuandtBraithwaiteaceae NEBell AENewton amp DQuandt Hypnodendra-ceae Broth Pterobryellaceae WRBuck amp Vitt Racopilaceae Kindb

Order Ptychomniales WRBuck CJCox AJShaw amp GoffinetPtychomniaceae MFleisch

Order Hookeriales MFleischDaltoniaceae Schimp Hookeriaceae Schimp HypopterygiaceaeMitt Leucomiaceae Broth Pilotrichaceae Kindb SaulomataceaeWRBuck CJCox AJShaw amp Goffinet Schimperobryaceae WR

17

Buck CJCox AJShaw amp GoffinetOrder Hypnales WRBuck amp Vitt

Amblystegiaceae GRoth Anomodontaceae Kindb BrachytheciaceaeSchimp Calliergonaceae Vanderpoorten Hedenaumls CJCox amp AJShaw Catagoniaceae WRBuck amp Ireland Climaciaceae KindbCryphaeaceae Schimp Echinodiaceae Broth Entodontaceae KindbFabroniaceae Schimp Fontinalaceae Schimp Helodiaceae OchyraHeterocladiaceae Ignatov amp Ignatova Hylocomiaceae MFleischHypnaceae Schimp Lembophyllaceae Broth LeptodontaceaeSchimp Lepyrodontaceae Broth Leskeaceae Schimp Leucodon-taceae Schimp Meteoriaceae Kindb Microtheciellaceae HAMillamp AJHarr Myriniaceae Schimp Myuriaceae MFleisch NeckeraceaeSchimp Orthorrhynchiaceae SHLin Phyllogoniaceae KindbPlagiotheciaceae MFleisch Pleuroziopsidaceae Ireland Prionodon-taceae Broth Pseudoleskeaceae Schimp PseudoleskeellaceaeIgnatov amp Ignatova Pterigynandraceae Schimp PterobryaceaeKindb Pylaisiaceae Schimp Pylaisiadelphaceae Goffinet amp WRBuck Regmatodontaceae Broth Rhytidiaceae Broth RigodiaceaeHACrum Rutenbergiaceae MFleisch Scorpidiaceae Ignatov ampIgnatova Sematophyllaceae Broth Sorapillaceae MFleisch Ste-reophyllaceae WRBuck amp Ireland Symphyodontaceae MFleischTheliaceae MFleisch Thuidiaceae Schimp TrachylomataceaeWRBuck amp Vitt

Acknowledgements

Sincere thanks are due to JLReveal (Ithaca) as well as WFPrudhomme van Reine and JFVeldkamp(Leiden) for comments and discussions about suprafamilial taxonomy to DQuandt (Dresden) for providingDNA from Rhacocarpus and Bartramiaceae species and to BGiesicke (Berlin) for technical assistance

References

BECKERT S H MUHLE D PRUCHNER amp V KNOOP (2001) The mitochondrial nad2 geneas a novel marker locus for phylogenetic analysis of early land plants a comparative analysis inmosses - Mol Phylogenet Evol 18 117-126

BELL NE amp AE NEWTON (2004) Systematic studies of non-hypnanaean pleurocarps establishinga phylogenetic framework for investigating the origins of pleurocarpy - In GOFFINET BV HOLLOWELL amp R MAGILL (eds) Molecular systematics of bryophytes Monogr Syst BotMissouri Bot Gard 98 290-319

BELL NE amp AE NEWTON (2007) Pleurocarpy in the Rhizogoniaceous grade - In NEWTONAE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolution SystematicsAssociation Special Volume Series 71 41-64

BELL NE D QUANDT TJ OBRIEN amp AE NEWTON (2007) Taxonomy and phylogeny inthe earliest diverging pleurocarps square holes and bifurcating pegs - Bryologist 110 533-560

BORSCH T KW HILU D QUANDT V WILDE C NEINHUIS amp W BARTHLOTT(2003) Non-coding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms- J Evol Biol 16 558-576

18

BUCK WR (2007) The history of pleurocarp classification two steps forward one step back - InNEWTON AE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 1-18

BUCK WR amp B GOFFINET (2000) Morphology and classification of mosses - In SHAWAJ amp B GOFFINET (eds) Bryophyte Biology pp 71-123 Cambridge University PressCambridge

CHIANG TY BA SCHAAL amp CI PENG (1998) Universal primers for amplification andsequencing a noncoding spacer between atpB and rbcL genes of chloroplast DNA - Bot Bull AcadSin 39 245-250

COX CJ B GOFFINET AE NEWTON AJ SHAW amp TAJ HEDDERSON (2000)Phylogenetic relationships among the diplolepideous-alternate mosses (Bryidae) inferred from nuclearand chloroplast DNA sequences - Bryologist 103 224-241

COX CJ B GOFFINET AJ SHAW amp SB BOLES (2004) Phylogenetic relationships amongthe mosses based on heterogeneous Bayesian analysis of multiple genes from multiple genomiccompartments - Syst Bot 29 234-250

CRANDALL-STOTLER B (1986) Morphogenesis developmental anatomy and bryophytephylogenetics contra-indications of monophyly - J Bryol 14 1-23

CROSBY MR RE MAGILL B ALLEN amp S HE (1999) A checklist of the mosses - MissouriBotanical Garden St Louis Missouri

DOWELD A (2001) Prosyllabus Tracheophytorum - GEOS Moscow i-lxxx + 110 pp

DOYLE JJ amp JL DOYLE (1990) Isolation of plant DNA from fresh tissue - Focus 12 13-15

DUFF RJ JC VILLAREAL DC CARGILL amp KS RENZAGLIA (2007) Progress andchallenges towards developing a phylogeny and classification of the hornworts - Bryologist 110214-243

FLEISCHER M (1920) Natuumlrliches System der Laubmoose - Hedwigia 61 390-400

FORREST LL EC DAVIS DG LONG BJ CRANDALL-STOTLER A CLARK ampML HOLLINGSWORTH (2006) Unraveling the evolutionary history of the liverworts (Marchantio-phyta) multiple taxa genomes and analyses - Bryologist 109 303-334

FRAHM J-P amp W FREY (1987) Moosflora 2 Aufl - UTB 1250 Stuttgart

FREY W (1977) Neue Vorstellungen uumlber die Verwandtschaftsgruppen und die Stammesgeschichteder Laubmoose - In FREY W H HURKA amp F OBERWINKLER (Hrsg) Beitraumlge zur Biologieder Pflanzen pp 117-139 Stuttgart

FREY W amp M STECH (2005) A morpho-molecular classification of the liverworts (Hepa-ticophytina Bryophyta) - Nova Hedwigia 81 55-78

FREY W M STECH amp K MEIszligNER (1999) Chloroplast DNA-relationship in palaeoaustralLopidium concinnum (Hypopterygiaceae Musci) An example of steno-evolution in mosses Studiesin austral temperate rain forest bryophytes 2 - Plant Syst Evol 218 67-75

GOFFINET B amp WR BUCK (2004) Systematics of Bryophyta (mosses) from molecules to arevised classification - In GOFFINET B V HOLLOWELL amp R MAGILL (eds) Molecularsystematics of bryophytes Monogr Syst Bot Missouri Bot Gard 98 205-239

GOFFINET B CJ COX AJ SHAW amp TAJ HEDDERSON (2001) The Bryophyta (mosses)Systematic and evolutionary inferences from an rps4 gene (cpDNA) phylogeny - Ann Bot 87191-208

GOFFINET B NJ WICKETT O WERNER RM ROS AJ SHAW amp CJ COX (2007)Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae(Bryophyta) - Ann Bot 99 747-753

19

GROTH-MALONEK M D PRUCHNER F GREWE amp V KNOOP (2005) Ancestors oftrans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosseswith vascular plants - Mol Biol Evol 22 117-125

HATTORI S amp H INOUE (1958) Preliminary report on Takakia lepidozioides - J Hattori BotLab 19 133-137

HE-NYGREacuteN X A JUSLEacuteN I AHONEN D GLENNY amp S PIIPPO (2006) Illuminating theevolutionary history of liverworts (Marchantiophyta) - towards a natural classification - Cladistics22 1-31

HEDDERSON TAJ DJ MURRAY CJ COX amp TL NOWELL (2004) Phylogeneticrelationships of haplolepideous mosses (Dicranidae) inferred from rps4 gene sequences - Syst Bot29 29-41

LA FARGE C BD MISHER JA WHEELER DP WALL K JOHANNES S SCHAFFERamp AJ SHAW (2000) Phylogenetic relationships within the haplolepideous mosses - Bryologist103 257-276

LA FARGE C AJ SHAW amp DH VITT (2002) The circumscription of the Dicranaceae(Bryopsida) based on the chloroplast regions trnL-trnF and rps4 - Syst Bot 27 435-452

MAGOMBO ZLK (2003) The phylogeny of basal peristomate mosses evidence from cpDNAand implications for peristome evolution - Syst Bot 28 24-38

MCNEILL J FR BARRIE HM BURDET V DEMOULIN DL HAWKSWORTHK MARHOLD DH NICOLSON J PRADO PC SILVA JE SKOG JH WIERSEMA ampNJ TURLAND (2006) International Code of Botanical Nomenclature (Vienna Code) - RegnumVegetabile 146 1-568

MUumlLLER K (2004) PRAP - computation of Bremer support for large data sets - Mol PhylogenetEvol 31 780-782

MUumlLLER K (2005) SeqState - primer design and sequence statistics for phylogenetic DNA datasets - Appl Bioinformatics 4 65-69

MUumlLLER K D QUANDT J MUumlLLER amp C NEINHUIS (2005) PhyDE v0992 PhylogeneticData Editor - httpwwwphydede

MURRAY BM (1988) Systematics of the Andreaeopsida (Bryophyta) two orders with links toTakakia - Nova Hedwigia Beih 90 289-336

NEWTON AE amp RS TANGNEY (eds) (2007) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 CRC Press Boca Raton 434 pp

NEWTON AE CJ COX JG DUCKETT JA WHEELER B GOFFINET TAJ HEDDER-SON amp BD MISHLER (2000) Evolution of the major moss lineages Phylogenetic analyses basedon multiple gene sequences and morphology - Bryologist 103 187-211

NEWTON AE N WIKSTROumlM NE BELL LL FORREST amp MS IGNATOV (2007)Dating the diversification of the pleurocarpous mosses - In NEWTON AE amp RS TANGNEY(eds) Pleurocarpous mosses systematics and evolution Systematics Association Special VolumeSeries 71 337-366

NIXON KC (1999) The parsimony ratchet a new method for rapid parsimony analysis - Cladistics15 407-411

OBRIEN TJ (2007) The phylogenetic distribution of pleurocarpous mosses evidence fromcpDNA sequences - In NEWTON AE amp RS TANGNEY (eds) Pleurocarpous mossessystematics and evolution Systematics Association Special Volume Series 71 19-41

OCHYRA R (2002) Nomenclatural changes in subfamilies of the Dicranaceae - CryptogamieBryol 23 345-349

20

OCHYRA R J ŻARNOWIEC amp H BEDNAREK-OCHYRA (2003) Census catalogue ofPolish mosses - Biodiv Poland 3 1-372

PEDERSEN N amp AE NEWTON (2007) Phylogenetic and morphological studies within thePtychomniales with emphasis on the evolution of dwarf males - In NEWTON AE amp RSTANGNEY (eds) Pleurocarpous mosses systematics and evolution Systematics AssociationSpecial Volume Series 71 367-392

QUANDT D amp M STECH (2005) Molecular evolution and secondary structure of the chloroplasttrnL intron in bryophytes - Mol Phylogenet Evol 36 429-443

QUANDT D K MUumlLLER amp S HUTTUNEN (2003) Characterisation of the chloroplast DNApsbT-H region and the influence of dyad symmetrical elements on phylogenetic reconstructions -Plant Biol 5 400-410

QUANDT D K MUumlLLER M STECH W FREY KW HILU amp T BORSCH (2004) Molecularevolution of the chloroplast trnL-F-region in land plants - In GOFFINET B V HOLLOWELL ampR MAGILL (eds) Molecular systematics of bryophytes Monogr Syst Bot Missouri Bot Gard98 13-37

QUANDT D NE BELL amp M STECH (2007) Unravelling the knot the Pulchrinodaceae famnov (Bryales) - In KUumlRSCHNER H T PFEIFFER amp M STECH (eds) A Festschrift to Wolf-gang Frey - a scientists life between deserts and rain forests Nova Hedwigia Beih 131 21-39

QIU Y-L Y CHO JC COX amp JD PALMER (1998) The gain of three mitochondrial intronsidentifies liverworts as the earliest land plants - Nature 394 671-674

QIU Y-L L LI B WANG Z CHEN V KNOOP M GROTH-MALONEK O DOM-BROVSKA J LEE L KENT J REST GF ESTABROOK TA HENDRY DW TAYLORCM TESTA M AMBROS B CRANDALL-STOTLER J DUFF M STECH W FREYD QUANDT amp CC DAVIS (2006) The deepest divergences in land plants inferred fromphylogenomic evidence - Proc Natl Acad Sci USA 103 15511-15516

RENZAGLIA KS S SCHUETTE RJ DUFF R LIGRONE AJ SHAW BD MISHLER ampJG DUCKETT (2007) Bryophyte phylogeny Advancing the molecular and morphological frontiers- Bryologist 110 179-213

SAMIGULLIN TH SP YACENTYUK GV DEGTYARYEVA KM VALIEJO-ROMANVK BOBROVA I CAPESIUS WF MARTIN AV TROITSKY VR FILIN amp ASANTONOV (2002) Paraphyly of bryophytes and close relationships of hornworts and vascularplants inferred from analysis of chloroplast rDNA ITS (cpITS) sequences - Arctoa 11 31-43

SANG T DJ CRAWFORD amp TF STUESSY (1997) Chloroplast DNA phylogeny reticulateevolution and biogeography of Paeonia (Paeoniaceae) - Amer J Bot 84 1120-1136

SHAW AJ amp KS RENZAGLIA (2004) Phylogeny and diversification of bryophytes - AmerJ Bot 91 1557-1581

SHAW AJ CJ COX amp B GOFFINET (2005) Global patterns of moss diversity taxonomic andmolecular inferences - Taxon 54 337-352

STECH M (1999a) A reclassification of Dicranaceae (Bryopsida) based on non-coding cpDNAsequence data - J Hattori Bot Lab 86 137-159

STECH M (1999b) A molecular systematic contribution to the position of Amphidium Schimp(Rhabdoweisiaceae Bryopsida) - Nova Hedwigia 68 291-300

STECH M (2004) Supraspecific circumscription and classification of Campylopus Brid(Dicranaceae Bryopsida) based on molecular data - Syst Bot 29 817-824

STECH M amp D QUANDT (2006) Molecular evolution of the chloroplast atpB-rbcL spacer inbryophytes - In SHARMA AK amp A SHARMA (eds) Plant Genome Biodiversity and EvolutionVol 2 Part B pp 409-431 Science Publishers Enfield New Hampshire

21

STECH M D QUANDT amp W FREY (2003) Molecular circumscription of the hornworts(Antho-cerotophyta) based on the chloroplast DNA trnL-trnF region - J Plant Res 116 389-398

STOTLER RE amp B CRANDALL-STOTLER (2005) A revised classification of theAnthocerotophyta and a checklist of the hornworts of North America north of Mexico - Bryologist108 16-26

SWOFFORD DL (2002) PAUP Phylogenetic analysis using parsimony (and other methods)version 40b10 - Sunderland MA

TABERLET P L GIELLY G PAUTOU amp J BOUVET (1991) Universal primers for amplificationof three non-coding regions of chloroplast DNA - Plant Mol Biol 17 1105-1109

TSUBOTA H Y AGENO B ESTEacuteBANEZ T YAMAGUCHI amp H DEGUCHI (2003)Molecular phylogeny of the Grimmiales (Musci) based on chloroplast rbcL sequences - Hikobia 1455-70

TSUBOTA H E DE LUNA D GONZAacuteLEZ MS IGNATOV amp H DEGUCHI (2004) Molecularphylogenetics and ordinal relationships based on analyses of a large-scale data set of 600 rbcLsequences of mosses - Hikobia 14 149-170

VITT DH (1984) Classification of the Bryopsida - In SCHUSTER RM (ed) New Manual ofBryology 2 696-759 Hattori Botanical Laboratory Nichinan Japan

VITT DH B GOFFINET amp T HEDDERSON (1998) 8 The ordinal classification of the mossesquestions and answers for the 1990s - In BATES JW NW ASHTON amp JG DUCKETT (eds)Bryology for the twenty-first century British Bryol Soc pp 113-123

Received 3 September 2007 accepted in revised form 30 October 2007

Page 12: botanica parcial 3

12

The molecular polyphyly of Rhizogoniaceae (eg Bell amp Newton 2004) was solvedby the transfer of rhizogonioid genera into broadly defined Aulacomniaceae andOrthodontiaceae (Bell et al 2007) which now include both acrocarpous andpleurocarpous taxa These systematic changes are also comprehensible by non-molecular characters such as morphological traits shared by Mesochaete andAulacomnium heterostichum (Hedw) Bruch amp Schimp or the variously reducedperistomes of Orthodontiaceae pp in contrast to the generally fully developed Bryum-type peristomes of rhizogonioid and hypnodendroid mosses (Bell et al 2007) Theposition of the solely pleurocarpous Hypnodendrales sister to the former Hypnidaeled to the recognition of the informal group core pleurocarps (Bell et al 2007)The former Hypnidae (Ptychomniales Hookeriales and Hypnales summarised ashomocostate pleurocarps) are monophyletic in most molecular analyses (eg Goffinetet al 2001 Tsubota et al 2004 Bell et al 2007) with Ptychomniales being well-supported (Pedersen amp Newton 2007 Table 2) Clarifying relationships betweenHookeriales and Hypnales and within the latter is still a challenge but recent molecularstudies seem to support a sister group relationship of both orders (Bell et al 2007present study)

Phylogenetic utility of non-coding plastid markers

Non-coding plastid markers that comprise both variable and conserved regionssuch as the trnL

UAA intron have repeatedly been shown to possess potential for

resolving relationships at high taxonomic levels (eg Borsch et al 2003 Quandtet al 2004) Both the trnL intron and atpB-rbcL spacer were characterised indetail in mosses with respect to their structure and molecular evolution (Quandt ampStech 2005 Stech amp Quandt 2006) They include conservative regions that can beunambiguosly aligned and even parts of the more variable regions can be used ifrepeats hairpin loops etc are correctly identified and adequately treated in thephylogenetic analyses (eg Quandt et al 2003 Quandt amp Stech 2005) Using theatpB-rbcL spacer alone (Stech amp Quandt 2006) relationships of the major mosslineages were largely consistent with the ldquototal evidencerdquo molecular tree of Goffinetamp Buck (2004) However in addition to general limitations that result from singlemarker analyses the use of non-coding markers may pose further problems suchas a high amount of homoplasy resulting in low resolution or low statistical supportfor many clades Therefore several recent molecular studies of relationships withinBryidae have employed both coding and non-coding markers (Table 2)Nevertheless the usefulness of analyses of combined non-coding plastid markerscannot be ruled out In fact Fig 1 and Table 2 indicate a phylogenetic signal inthe present data set as many clades are recovered that are usually also resolvedin analyses of coding or combined coding and non-coding markers Especiallywith regard to statistical support however the present analysis is inferior tothose of other recent data sets especially Bell et al (2007) and Quandt et al(2007) In addition the non-coding markers used here are of different suitabilityand even the two intergenic spacers differ considerably from each other ThepsbA-trnH spacer contributes much less to the trees resolution than the atpB-rbcL spacer first because it is much shorter and second because relatively largeparts are attributed to hairpin loops or otherwise hypervariable regions These

13

results indicate that future studies should evaluate the molecular evolution andphylogenetic potential of new markers both coding and con-coding and choosethe most suitable ones in a combined analysis to resolve the remaining uncertaintiesin moss phylogeny

Taxonomy

Takakiaceae Stech amp WFrey stat nov

Plantae virides nusquam rhizophorae sine protonemate e caudicis rhizomatis erectae Caudicesrhizomati et axes geotropi radiformes frequenter intercalariter ramificantes sine phyllidiis cumpapillis mucilaginis rostratis Caules phyllidiiferi saepe furcati Phyllidia sine lamina et costadistincta profunde 2-4(-5)-lobata pluristratosa tristicha sed torsione spiraliter disposita Filumcentralium in ambabus generationibus (axibus gametophyti et setis) adest Plantae dioicae Antheridiaet archegonia nuda Sporophytum terminale solitarium Seta persistens Capsula tortilis admaturitatem schizocarpa secus unam rimam spiralem longitudinalem dehiscens Stomata etoperculum absunt peristomium nullum Calyptra mitriformis

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiaceae SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval (Art 411)

Takakiales Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiales SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval

Takakiales SHatt amp Inoue ex RMSchust J Hattori Bot Lab 26 224 1963 nom inval (cumdescr latin)

Takakiopsida Stech amp WFrey statnov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiopsida Goffinet amp WRBuck Monogr Syst Bot Missouri Bot Gard 98 232 2004 nominval

Takakiopsida Jia et al Acta Phytotax Sin 41 350 351 2003 nom nud

Takakiopsida Wang amp Wu Fl Bryophyt Sin 8 447 2004 nom inval (cum descr latin)

Takakiophytina Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue JHattori Bot Lab 19 137 1958

Gigaspermidae Stech amp WFrey subclass nov

Plantae acrocarpae terrestres stoloniferae ramis brevibus erectis Folia unicostata cellulis laxislaevibus Capsula plerumque valde rugosa gymnostomatica vel cleistocarpa stomata cum duabuscellulis sociis Ab Funariidis et Encalyptidis charactere phylogenomico (71-kb inversio abest)separatae

14

TYPUS Gigaspermum Lindb Oumlfversigt af Foumlrhandlingar Kongl Svenska Vetenskaps-Akademien21 599 1865

Amphidiaceae Stech stat nov

Based on Dicranaceae subfam Amphidioideae Ochyra in Ochyra Zarnowiec amp Bednarek-OchyraCens Cat Polish Mosses 110 2003

TYPUS Amphidium Schimp Coroll Bryol Eur 39 1856

Amphidiaceae AJESm Moss Fl Britain Ireland 2nd ed 657 2004 nom inval descr angl

Dicranellaceae Stech stat nov

Based on Dicranaceae subfam Dicranelloideae Lindb Utkast Eur Bladmoss 33 1878[lsquoUnderfamilje Dicranelleaersquo]

TYPUS Dicranella (MuumlllHal) Schimp Coroll Bryol Eur 13 1856

Oncophoraceae Stech stat nov

Based on Dicranaceae subfam Oncophoroideae Lindb Utkast Eur Bladmoss 34 1878[lsquoUnderfamilje Oncophoreaersquo]

TYPUS Oncophorus (Brid) Brid Bryol Univ 1 389 1826

Hypodontiaceae Stech fam nov

Plantae robustae characteribus morphologicis Pottiaceis et Calymperaceis similes sedcharacteribus molecularicis separatae Bracteae perichaetiales internae e basi vaginantes subulataevel aristatae Capsula aspectu succulenta cellulae exothecii incrassatae annulus magnopereabsens Peristomii dentes breves triangulati incurvati aurantiaci leves vel infirme verrucosiCalyptra cucullata

TYPUS Hypodontium MuumlllHal Hedwigia 38 96 1899

Helicophyllales Stech amp WFrey ord nov

Plantae acrocarpae prostratae tomentosae Folia dimorpha in duas series laterales et unam seriemventralem divisa Costa percurrens Cellulae hexagonae ad subquadratae papillosae Capsula immersacupulata ad oblonga infra orificium abrupte incurvata stomata destituta Peristomium nullum Sporaeisomorphae heteropolares granulatae

TYPUS Helicophyllum Brid Bryol Univ 2 771 1827

Synopsis of the suprageneric classification of BryophytaAuthor citations are in accordance with Art 492 of the Vienna Code (McNeill et al 2006)

Subdivision Takakiophytina Stech amp WFreyClass Takakiopsida Stech amp WFrey

Order Takakiales Stech amp WFreyTakakiaceae Stech amp WFrey

Subdivision Sphagnophytina DoweldClass Sphagnopsida Schimp

Order Sphagnales Limpr

15

Sphagnaceae DumortOrder Ambuchananiales Seppelt amp HACrum

Ambuchananiaceae Seppelt amp HACrumSubdivision Bryophytina Engler

Class Andreaeopsida JHSchaffnSubclass Andreaeidae Engl

Order Andreaeales LimprAndreaeaceae Dumort

Subclass Andreaeobryidae OchyraOrder Andreaeobryales BMMurray

Andreaeobryaceae Steere amp BMMurrayClass Oedipodiopsida Goffinet amp WRBuck

Order Oedipodiales Goffinet amp WRBuckOedipodiaceae Schimp

Class Tetraphidopsida Goffinet amp WRBuckOrder Tetraphidales MFleisch

Tetraphidaceae SchimpClass Polytrichopsida Doweld

Order Polytrichales MFleischPolytrichaceae Schwaumlgr

Class Bryopsida PaxSubclass Buxbaumiidae Doweld

Order Buxbaumiales MFleischBuxbaumiaceae Schimp

Subclass Diphysciidae OchyraOrder Diphysciales MFleisch

Diphysciaceae MFleischSubclass Timmiidae Ochyra

Order Timmiales OchyraTimmiaceae Schimp

Subclass Encalyptidae Ochyra Żarnowiec amp Bednarek-OchyraOrder Encalyptales Dixon

Encalyptaceae SchimpSubclass Funariidae Ochyra

Order Funariales MFleischFunariaceae Schwaumlgr Disceliaceae Schimp

Subclass Gigaspermidae Stech amp WFreyOrder Gigaspermales Goffinet Wickett OWerner Ros AJShaw amp CJCox

Gigaspermaceae LindbSubclass Dicranidae Doweld

Order Catoscopiales Ignatov amp IgnatovaCatoscopiaceae Broth

Order Scouleriales Goffinet amp WRBuckDrummondiaceae Goffinet Scouleriaceae SPChurchill

Order Bryoxiphiales HACrum amp LEAndersonBryoxiphiaceae Besch

16

Order Grimmiales MFleischGrimmiaceae Arn Ptychomitriaceae Schimp Seligeriaceae Schimp

Order Archidiales LimprArchidiaceae Schimp

Order Mitteniales ShawMitteniaceae Broth

Order Dicranales HPhilib ex MFleischAmphidiaceae Stech Aongstroemiaceae De Not BruchiaceaeSchimp Calymperaceae Kindb Dicranaceae Schimp Dicranel-laceae Stech Ditrichaceae Limpr Erpodiaceae Broth EustichiaceaeBroth Fissidentaceae Schimp Leucobryaceae Schimp Onco-phoraceae Stech Rhachitheciaceae HRob Schistostegaceae SchimpViridivelleraceae IGStone Wardiaceae Welch

Order Pottiales MFleischEphemeraceae Schimp Hypodontiaceae Stech PleurophascaceaeBroth Pottiaceae Schimp Serpotortellaceae WDReese amp RHZander

Subclass Bryidae EnglOrder Hedwigiales Ochyra

Hedwigiaceae Schimp Rhacocarpaceae KindbOrder Helicophyllales Stech amp WFrey

Helicophyllaceae BrothOrder Bartramiales DQuandt NEBell amp Stech

Bartramiaceae SchwaumlgrOrder Splachnales Ochyra

Meesiaceae Schimp Splachnaceae Grev amp ArnOrder Bryales Limpr

Bryaceae Schwaumlgr Leptostomataceae Schwaumlgr Mniaceae SchwaumlgrPhyllodrepaniaceae Crosby Pseudoditrichaceae Steere amp ZIwatsPulchrinodaceae DQuandt NEBell amp Stech

Order Orthotrichales DixonOrthotrichaceae Arn

Order Orthodontiales NEBell AENewton amp DQuandtOrthodontiaceae Goffinet

Order Aulacomniales NEBell AENewton amp DQuandtAulacomniaceae Schimp

Order Rhizogoniales Goffinet amp WRBuckRhizogoniaceae Broth

Order Hypnodendrales NEBell AENewton amp DQuandtBraithwaiteaceae NEBell AENewton amp DQuandt Hypnodendra-ceae Broth Pterobryellaceae WRBuck amp Vitt Racopilaceae Kindb

Order Ptychomniales WRBuck CJCox AJShaw amp GoffinetPtychomniaceae MFleisch

Order Hookeriales MFleischDaltoniaceae Schimp Hookeriaceae Schimp HypopterygiaceaeMitt Leucomiaceae Broth Pilotrichaceae Kindb SaulomataceaeWRBuck CJCox AJShaw amp Goffinet Schimperobryaceae WR

17

Buck CJCox AJShaw amp GoffinetOrder Hypnales WRBuck amp Vitt

Amblystegiaceae GRoth Anomodontaceae Kindb BrachytheciaceaeSchimp Calliergonaceae Vanderpoorten Hedenaumls CJCox amp AJShaw Catagoniaceae WRBuck amp Ireland Climaciaceae KindbCryphaeaceae Schimp Echinodiaceae Broth Entodontaceae KindbFabroniaceae Schimp Fontinalaceae Schimp Helodiaceae OchyraHeterocladiaceae Ignatov amp Ignatova Hylocomiaceae MFleischHypnaceae Schimp Lembophyllaceae Broth LeptodontaceaeSchimp Lepyrodontaceae Broth Leskeaceae Schimp Leucodon-taceae Schimp Meteoriaceae Kindb Microtheciellaceae HAMillamp AJHarr Myriniaceae Schimp Myuriaceae MFleisch NeckeraceaeSchimp Orthorrhynchiaceae SHLin Phyllogoniaceae KindbPlagiotheciaceae MFleisch Pleuroziopsidaceae Ireland Prionodon-taceae Broth Pseudoleskeaceae Schimp PseudoleskeellaceaeIgnatov amp Ignatova Pterigynandraceae Schimp PterobryaceaeKindb Pylaisiaceae Schimp Pylaisiadelphaceae Goffinet amp WRBuck Regmatodontaceae Broth Rhytidiaceae Broth RigodiaceaeHACrum Rutenbergiaceae MFleisch Scorpidiaceae Ignatov ampIgnatova Sematophyllaceae Broth Sorapillaceae MFleisch Ste-reophyllaceae WRBuck amp Ireland Symphyodontaceae MFleischTheliaceae MFleisch Thuidiaceae Schimp TrachylomataceaeWRBuck amp Vitt

Acknowledgements

Sincere thanks are due to JLReveal (Ithaca) as well as WFPrudhomme van Reine and JFVeldkamp(Leiden) for comments and discussions about suprafamilial taxonomy to DQuandt (Dresden) for providingDNA from Rhacocarpus and Bartramiaceae species and to BGiesicke (Berlin) for technical assistance

References

BECKERT S H MUHLE D PRUCHNER amp V KNOOP (2001) The mitochondrial nad2 geneas a novel marker locus for phylogenetic analysis of early land plants a comparative analysis inmosses - Mol Phylogenet Evol 18 117-126

BELL NE amp AE NEWTON (2004) Systematic studies of non-hypnanaean pleurocarps establishinga phylogenetic framework for investigating the origins of pleurocarpy - In GOFFINET BV HOLLOWELL amp R MAGILL (eds) Molecular systematics of bryophytes Monogr Syst BotMissouri Bot Gard 98 290-319

BELL NE amp AE NEWTON (2007) Pleurocarpy in the Rhizogoniaceous grade - In NEWTONAE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolution SystematicsAssociation Special Volume Series 71 41-64

BELL NE D QUANDT TJ OBRIEN amp AE NEWTON (2007) Taxonomy and phylogeny inthe earliest diverging pleurocarps square holes and bifurcating pegs - Bryologist 110 533-560

BORSCH T KW HILU D QUANDT V WILDE C NEINHUIS amp W BARTHLOTT(2003) Non-coding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms- J Evol Biol 16 558-576

18

BUCK WR (2007) The history of pleurocarp classification two steps forward one step back - InNEWTON AE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 1-18

BUCK WR amp B GOFFINET (2000) Morphology and classification of mosses - In SHAWAJ amp B GOFFINET (eds) Bryophyte Biology pp 71-123 Cambridge University PressCambridge

CHIANG TY BA SCHAAL amp CI PENG (1998) Universal primers for amplification andsequencing a noncoding spacer between atpB and rbcL genes of chloroplast DNA - Bot Bull AcadSin 39 245-250

COX CJ B GOFFINET AE NEWTON AJ SHAW amp TAJ HEDDERSON (2000)Phylogenetic relationships among the diplolepideous-alternate mosses (Bryidae) inferred from nuclearand chloroplast DNA sequences - Bryologist 103 224-241

COX CJ B GOFFINET AJ SHAW amp SB BOLES (2004) Phylogenetic relationships amongthe mosses based on heterogeneous Bayesian analysis of multiple genes from multiple genomiccompartments - Syst Bot 29 234-250

CRANDALL-STOTLER B (1986) Morphogenesis developmental anatomy and bryophytephylogenetics contra-indications of monophyly - J Bryol 14 1-23

CROSBY MR RE MAGILL B ALLEN amp S HE (1999) A checklist of the mosses - MissouriBotanical Garden St Louis Missouri

DOWELD A (2001) Prosyllabus Tracheophytorum - GEOS Moscow i-lxxx + 110 pp

DOYLE JJ amp JL DOYLE (1990) Isolation of plant DNA from fresh tissue - Focus 12 13-15

DUFF RJ JC VILLAREAL DC CARGILL amp KS RENZAGLIA (2007) Progress andchallenges towards developing a phylogeny and classification of the hornworts - Bryologist 110214-243

FLEISCHER M (1920) Natuumlrliches System der Laubmoose - Hedwigia 61 390-400

FORREST LL EC DAVIS DG LONG BJ CRANDALL-STOTLER A CLARK ampML HOLLINGSWORTH (2006) Unraveling the evolutionary history of the liverworts (Marchantio-phyta) multiple taxa genomes and analyses - Bryologist 109 303-334

FRAHM J-P amp W FREY (1987) Moosflora 2 Aufl - UTB 1250 Stuttgart

FREY W (1977) Neue Vorstellungen uumlber die Verwandtschaftsgruppen und die Stammesgeschichteder Laubmoose - In FREY W H HURKA amp F OBERWINKLER (Hrsg) Beitraumlge zur Biologieder Pflanzen pp 117-139 Stuttgart

FREY W amp M STECH (2005) A morpho-molecular classification of the liverworts (Hepa-ticophytina Bryophyta) - Nova Hedwigia 81 55-78

FREY W M STECH amp K MEIszligNER (1999) Chloroplast DNA-relationship in palaeoaustralLopidium concinnum (Hypopterygiaceae Musci) An example of steno-evolution in mosses Studiesin austral temperate rain forest bryophytes 2 - Plant Syst Evol 218 67-75

GOFFINET B amp WR BUCK (2004) Systematics of Bryophyta (mosses) from molecules to arevised classification - In GOFFINET B V HOLLOWELL amp R MAGILL (eds) Molecularsystematics of bryophytes Monogr Syst Bot Missouri Bot Gard 98 205-239

GOFFINET B CJ COX AJ SHAW amp TAJ HEDDERSON (2001) The Bryophyta (mosses)Systematic and evolutionary inferences from an rps4 gene (cpDNA) phylogeny - Ann Bot 87191-208

GOFFINET B NJ WICKETT O WERNER RM ROS AJ SHAW amp CJ COX (2007)Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae(Bryophyta) - Ann Bot 99 747-753

19

GROTH-MALONEK M D PRUCHNER F GREWE amp V KNOOP (2005) Ancestors oftrans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosseswith vascular plants - Mol Biol Evol 22 117-125

HATTORI S amp H INOUE (1958) Preliminary report on Takakia lepidozioides - J Hattori BotLab 19 133-137

HE-NYGREacuteN X A JUSLEacuteN I AHONEN D GLENNY amp S PIIPPO (2006) Illuminating theevolutionary history of liverworts (Marchantiophyta) - towards a natural classification - Cladistics22 1-31

HEDDERSON TAJ DJ MURRAY CJ COX amp TL NOWELL (2004) Phylogeneticrelationships of haplolepideous mosses (Dicranidae) inferred from rps4 gene sequences - Syst Bot29 29-41

LA FARGE C BD MISHER JA WHEELER DP WALL K JOHANNES S SCHAFFERamp AJ SHAW (2000) Phylogenetic relationships within the haplolepideous mosses - Bryologist103 257-276

LA FARGE C AJ SHAW amp DH VITT (2002) The circumscription of the Dicranaceae(Bryopsida) based on the chloroplast regions trnL-trnF and rps4 - Syst Bot 27 435-452

MAGOMBO ZLK (2003) The phylogeny of basal peristomate mosses evidence from cpDNAand implications for peristome evolution - Syst Bot 28 24-38

MCNEILL J FR BARRIE HM BURDET V DEMOULIN DL HAWKSWORTHK MARHOLD DH NICOLSON J PRADO PC SILVA JE SKOG JH WIERSEMA ampNJ TURLAND (2006) International Code of Botanical Nomenclature (Vienna Code) - RegnumVegetabile 146 1-568

MUumlLLER K (2004) PRAP - computation of Bremer support for large data sets - Mol PhylogenetEvol 31 780-782

MUumlLLER K (2005) SeqState - primer design and sequence statistics for phylogenetic DNA datasets - Appl Bioinformatics 4 65-69

MUumlLLER K D QUANDT J MUumlLLER amp C NEINHUIS (2005) PhyDE v0992 PhylogeneticData Editor - httpwwwphydede

MURRAY BM (1988) Systematics of the Andreaeopsida (Bryophyta) two orders with links toTakakia - Nova Hedwigia Beih 90 289-336

NEWTON AE amp RS TANGNEY (eds) (2007) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 CRC Press Boca Raton 434 pp

NEWTON AE CJ COX JG DUCKETT JA WHEELER B GOFFINET TAJ HEDDER-SON amp BD MISHLER (2000) Evolution of the major moss lineages Phylogenetic analyses basedon multiple gene sequences and morphology - Bryologist 103 187-211

NEWTON AE N WIKSTROumlM NE BELL LL FORREST amp MS IGNATOV (2007)Dating the diversification of the pleurocarpous mosses - In NEWTON AE amp RS TANGNEY(eds) Pleurocarpous mosses systematics and evolution Systematics Association Special VolumeSeries 71 337-366

NIXON KC (1999) The parsimony ratchet a new method for rapid parsimony analysis - Cladistics15 407-411

OBRIEN TJ (2007) The phylogenetic distribution of pleurocarpous mosses evidence fromcpDNA sequences - In NEWTON AE amp RS TANGNEY (eds) Pleurocarpous mossessystematics and evolution Systematics Association Special Volume Series 71 19-41

OCHYRA R (2002) Nomenclatural changes in subfamilies of the Dicranaceae - CryptogamieBryol 23 345-349

20

OCHYRA R J ŻARNOWIEC amp H BEDNAREK-OCHYRA (2003) Census catalogue ofPolish mosses - Biodiv Poland 3 1-372

PEDERSEN N amp AE NEWTON (2007) Phylogenetic and morphological studies within thePtychomniales with emphasis on the evolution of dwarf males - In NEWTON AE amp RSTANGNEY (eds) Pleurocarpous mosses systematics and evolution Systematics AssociationSpecial Volume Series 71 367-392

QUANDT D amp M STECH (2005) Molecular evolution and secondary structure of the chloroplasttrnL intron in bryophytes - Mol Phylogenet Evol 36 429-443

QUANDT D K MUumlLLER amp S HUTTUNEN (2003) Characterisation of the chloroplast DNApsbT-H region and the influence of dyad symmetrical elements on phylogenetic reconstructions -Plant Biol 5 400-410

QUANDT D K MUumlLLER M STECH W FREY KW HILU amp T BORSCH (2004) Molecularevolution of the chloroplast trnL-F-region in land plants - In GOFFINET B V HOLLOWELL ampR MAGILL (eds) Molecular systematics of bryophytes Monogr Syst Bot Missouri Bot Gard98 13-37

QUANDT D NE BELL amp M STECH (2007) Unravelling the knot the Pulchrinodaceae famnov (Bryales) - In KUumlRSCHNER H T PFEIFFER amp M STECH (eds) A Festschrift to Wolf-gang Frey - a scientists life between deserts and rain forests Nova Hedwigia Beih 131 21-39

QIU Y-L Y CHO JC COX amp JD PALMER (1998) The gain of three mitochondrial intronsidentifies liverworts as the earliest land plants - Nature 394 671-674

QIU Y-L L LI B WANG Z CHEN V KNOOP M GROTH-MALONEK O DOM-BROVSKA J LEE L KENT J REST GF ESTABROOK TA HENDRY DW TAYLORCM TESTA M AMBROS B CRANDALL-STOTLER J DUFF M STECH W FREYD QUANDT amp CC DAVIS (2006) The deepest divergences in land plants inferred fromphylogenomic evidence - Proc Natl Acad Sci USA 103 15511-15516

RENZAGLIA KS S SCHUETTE RJ DUFF R LIGRONE AJ SHAW BD MISHLER ampJG DUCKETT (2007) Bryophyte phylogeny Advancing the molecular and morphological frontiers- Bryologist 110 179-213

SAMIGULLIN TH SP YACENTYUK GV DEGTYARYEVA KM VALIEJO-ROMANVK BOBROVA I CAPESIUS WF MARTIN AV TROITSKY VR FILIN amp ASANTONOV (2002) Paraphyly of bryophytes and close relationships of hornworts and vascularplants inferred from analysis of chloroplast rDNA ITS (cpITS) sequences - Arctoa 11 31-43

SANG T DJ CRAWFORD amp TF STUESSY (1997) Chloroplast DNA phylogeny reticulateevolution and biogeography of Paeonia (Paeoniaceae) - Amer J Bot 84 1120-1136

SHAW AJ amp KS RENZAGLIA (2004) Phylogeny and diversification of bryophytes - AmerJ Bot 91 1557-1581

SHAW AJ CJ COX amp B GOFFINET (2005) Global patterns of moss diversity taxonomic andmolecular inferences - Taxon 54 337-352

STECH M (1999a) A reclassification of Dicranaceae (Bryopsida) based on non-coding cpDNAsequence data - J Hattori Bot Lab 86 137-159

STECH M (1999b) A molecular systematic contribution to the position of Amphidium Schimp(Rhabdoweisiaceae Bryopsida) - Nova Hedwigia 68 291-300

STECH M (2004) Supraspecific circumscription and classification of Campylopus Brid(Dicranaceae Bryopsida) based on molecular data - Syst Bot 29 817-824

STECH M amp D QUANDT (2006) Molecular evolution of the chloroplast atpB-rbcL spacer inbryophytes - In SHARMA AK amp A SHARMA (eds) Plant Genome Biodiversity and EvolutionVol 2 Part B pp 409-431 Science Publishers Enfield New Hampshire

21

STECH M D QUANDT amp W FREY (2003) Molecular circumscription of the hornworts(Antho-cerotophyta) based on the chloroplast DNA trnL-trnF region - J Plant Res 116 389-398

STOTLER RE amp B CRANDALL-STOTLER (2005) A revised classification of theAnthocerotophyta and a checklist of the hornworts of North America north of Mexico - Bryologist108 16-26

SWOFFORD DL (2002) PAUP Phylogenetic analysis using parsimony (and other methods)version 40b10 - Sunderland MA

TABERLET P L GIELLY G PAUTOU amp J BOUVET (1991) Universal primers for amplificationof three non-coding regions of chloroplast DNA - Plant Mol Biol 17 1105-1109

TSUBOTA H Y AGENO B ESTEacuteBANEZ T YAMAGUCHI amp H DEGUCHI (2003)Molecular phylogeny of the Grimmiales (Musci) based on chloroplast rbcL sequences - Hikobia 1455-70

TSUBOTA H E DE LUNA D GONZAacuteLEZ MS IGNATOV amp H DEGUCHI (2004) Molecularphylogenetics and ordinal relationships based on analyses of a large-scale data set of 600 rbcLsequences of mosses - Hikobia 14 149-170

VITT DH (1984) Classification of the Bryopsida - In SCHUSTER RM (ed) New Manual ofBryology 2 696-759 Hattori Botanical Laboratory Nichinan Japan

VITT DH B GOFFINET amp T HEDDERSON (1998) 8 The ordinal classification of the mossesquestions and answers for the 1990s - In BATES JW NW ASHTON amp JG DUCKETT (eds)Bryology for the twenty-first century British Bryol Soc pp 113-123

Received 3 September 2007 accepted in revised form 30 October 2007

Page 13: botanica parcial 3

13

results indicate that future studies should evaluate the molecular evolution andphylogenetic potential of new markers both coding and con-coding and choosethe most suitable ones in a combined analysis to resolve the remaining uncertaintiesin moss phylogeny

Taxonomy

Takakiaceae Stech amp WFrey stat nov

Plantae virides nusquam rhizophorae sine protonemate e caudicis rhizomatis erectae Caudicesrhizomati et axes geotropi radiformes frequenter intercalariter ramificantes sine phyllidiis cumpapillis mucilaginis rostratis Caules phyllidiiferi saepe furcati Phyllidia sine lamina et costadistincta profunde 2-4(-5)-lobata pluristratosa tristicha sed torsione spiraliter disposita Filumcentralium in ambabus generationibus (axibus gametophyti et setis) adest Plantae dioicae Antheridiaet archegonia nuda Sporophytum terminale solitarium Seta persistens Capsula tortilis admaturitatem schizocarpa secus unam rimam spiralem longitudinalem dehiscens Stomata etoperculum absunt peristomium nullum Calyptra mitriformis

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiaceae SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval (Art 411)

Takakiales Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiales SHatt amp Inoue J Hattori Bot Lab 19 137 1958 nom inval

Takakiales SHatt amp Inoue ex RMSchust J Hattori Bot Lab 26 224 1963 nom inval (cumdescr latin)

Takakiopsida Stech amp WFrey statnov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue J Hattori Bot Lab 19 137 1958

Takakiopsida Goffinet amp WRBuck Monogr Syst Bot Missouri Bot Gard 98 232 2004 nominval

Takakiopsida Jia et al Acta Phytotax Sin 41 350 351 2003 nom nud

Takakiopsida Wang amp Wu Fl Bryophyt Sin 8 447 2004 nom inval (cum descr latin)

Takakiophytina Stech amp WFrey stat nov

Based on Takakiaceae Stech amp WFrey Nova Hedwigia 86 13 2008

TYPUS Takakia SHatt amp Inoue JHattori Bot Lab 19 137 1958

Gigaspermidae Stech amp WFrey subclass nov

Plantae acrocarpae terrestres stoloniferae ramis brevibus erectis Folia unicostata cellulis laxislaevibus Capsula plerumque valde rugosa gymnostomatica vel cleistocarpa stomata cum duabuscellulis sociis Ab Funariidis et Encalyptidis charactere phylogenomico (71-kb inversio abest)separatae

14

TYPUS Gigaspermum Lindb Oumlfversigt af Foumlrhandlingar Kongl Svenska Vetenskaps-Akademien21 599 1865

Amphidiaceae Stech stat nov

Based on Dicranaceae subfam Amphidioideae Ochyra in Ochyra Zarnowiec amp Bednarek-OchyraCens Cat Polish Mosses 110 2003

TYPUS Amphidium Schimp Coroll Bryol Eur 39 1856

Amphidiaceae AJESm Moss Fl Britain Ireland 2nd ed 657 2004 nom inval descr angl

Dicranellaceae Stech stat nov

Based on Dicranaceae subfam Dicranelloideae Lindb Utkast Eur Bladmoss 33 1878[lsquoUnderfamilje Dicranelleaersquo]

TYPUS Dicranella (MuumlllHal) Schimp Coroll Bryol Eur 13 1856

Oncophoraceae Stech stat nov

Based on Dicranaceae subfam Oncophoroideae Lindb Utkast Eur Bladmoss 34 1878[lsquoUnderfamilje Oncophoreaersquo]

TYPUS Oncophorus (Brid) Brid Bryol Univ 1 389 1826

Hypodontiaceae Stech fam nov

Plantae robustae characteribus morphologicis Pottiaceis et Calymperaceis similes sedcharacteribus molecularicis separatae Bracteae perichaetiales internae e basi vaginantes subulataevel aristatae Capsula aspectu succulenta cellulae exothecii incrassatae annulus magnopereabsens Peristomii dentes breves triangulati incurvati aurantiaci leves vel infirme verrucosiCalyptra cucullata

TYPUS Hypodontium MuumlllHal Hedwigia 38 96 1899

Helicophyllales Stech amp WFrey ord nov

Plantae acrocarpae prostratae tomentosae Folia dimorpha in duas series laterales et unam seriemventralem divisa Costa percurrens Cellulae hexagonae ad subquadratae papillosae Capsula immersacupulata ad oblonga infra orificium abrupte incurvata stomata destituta Peristomium nullum Sporaeisomorphae heteropolares granulatae

TYPUS Helicophyllum Brid Bryol Univ 2 771 1827

Synopsis of the suprageneric classification of BryophytaAuthor citations are in accordance with Art 492 of the Vienna Code (McNeill et al 2006)

Subdivision Takakiophytina Stech amp WFreyClass Takakiopsida Stech amp WFrey

Order Takakiales Stech amp WFreyTakakiaceae Stech amp WFrey

Subdivision Sphagnophytina DoweldClass Sphagnopsida Schimp

Order Sphagnales Limpr

15

Sphagnaceae DumortOrder Ambuchananiales Seppelt amp HACrum

Ambuchananiaceae Seppelt amp HACrumSubdivision Bryophytina Engler

Class Andreaeopsida JHSchaffnSubclass Andreaeidae Engl

Order Andreaeales LimprAndreaeaceae Dumort

Subclass Andreaeobryidae OchyraOrder Andreaeobryales BMMurray

Andreaeobryaceae Steere amp BMMurrayClass Oedipodiopsida Goffinet amp WRBuck

Order Oedipodiales Goffinet amp WRBuckOedipodiaceae Schimp

Class Tetraphidopsida Goffinet amp WRBuckOrder Tetraphidales MFleisch

Tetraphidaceae SchimpClass Polytrichopsida Doweld

Order Polytrichales MFleischPolytrichaceae Schwaumlgr

Class Bryopsida PaxSubclass Buxbaumiidae Doweld

Order Buxbaumiales MFleischBuxbaumiaceae Schimp

Subclass Diphysciidae OchyraOrder Diphysciales MFleisch

Diphysciaceae MFleischSubclass Timmiidae Ochyra

Order Timmiales OchyraTimmiaceae Schimp

Subclass Encalyptidae Ochyra Żarnowiec amp Bednarek-OchyraOrder Encalyptales Dixon

Encalyptaceae SchimpSubclass Funariidae Ochyra

Order Funariales MFleischFunariaceae Schwaumlgr Disceliaceae Schimp

Subclass Gigaspermidae Stech amp WFreyOrder Gigaspermales Goffinet Wickett OWerner Ros AJShaw amp CJCox

Gigaspermaceae LindbSubclass Dicranidae Doweld

Order Catoscopiales Ignatov amp IgnatovaCatoscopiaceae Broth

Order Scouleriales Goffinet amp WRBuckDrummondiaceae Goffinet Scouleriaceae SPChurchill

Order Bryoxiphiales HACrum amp LEAndersonBryoxiphiaceae Besch

16

Order Grimmiales MFleischGrimmiaceae Arn Ptychomitriaceae Schimp Seligeriaceae Schimp

Order Archidiales LimprArchidiaceae Schimp

Order Mitteniales ShawMitteniaceae Broth

Order Dicranales HPhilib ex MFleischAmphidiaceae Stech Aongstroemiaceae De Not BruchiaceaeSchimp Calymperaceae Kindb Dicranaceae Schimp Dicranel-laceae Stech Ditrichaceae Limpr Erpodiaceae Broth EustichiaceaeBroth Fissidentaceae Schimp Leucobryaceae Schimp Onco-phoraceae Stech Rhachitheciaceae HRob Schistostegaceae SchimpViridivelleraceae IGStone Wardiaceae Welch

Order Pottiales MFleischEphemeraceae Schimp Hypodontiaceae Stech PleurophascaceaeBroth Pottiaceae Schimp Serpotortellaceae WDReese amp RHZander

Subclass Bryidae EnglOrder Hedwigiales Ochyra

Hedwigiaceae Schimp Rhacocarpaceae KindbOrder Helicophyllales Stech amp WFrey

Helicophyllaceae BrothOrder Bartramiales DQuandt NEBell amp Stech

Bartramiaceae SchwaumlgrOrder Splachnales Ochyra

Meesiaceae Schimp Splachnaceae Grev amp ArnOrder Bryales Limpr

Bryaceae Schwaumlgr Leptostomataceae Schwaumlgr Mniaceae SchwaumlgrPhyllodrepaniaceae Crosby Pseudoditrichaceae Steere amp ZIwatsPulchrinodaceae DQuandt NEBell amp Stech

Order Orthotrichales DixonOrthotrichaceae Arn

Order Orthodontiales NEBell AENewton amp DQuandtOrthodontiaceae Goffinet

Order Aulacomniales NEBell AENewton amp DQuandtAulacomniaceae Schimp

Order Rhizogoniales Goffinet amp WRBuckRhizogoniaceae Broth

Order Hypnodendrales NEBell AENewton amp DQuandtBraithwaiteaceae NEBell AENewton amp DQuandt Hypnodendra-ceae Broth Pterobryellaceae WRBuck amp Vitt Racopilaceae Kindb

Order Ptychomniales WRBuck CJCox AJShaw amp GoffinetPtychomniaceae MFleisch

Order Hookeriales MFleischDaltoniaceae Schimp Hookeriaceae Schimp HypopterygiaceaeMitt Leucomiaceae Broth Pilotrichaceae Kindb SaulomataceaeWRBuck CJCox AJShaw amp Goffinet Schimperobryaceae WR

17

Buck CJCox AJShaw amp GoffinetOrder Hypnales WRBuck amp Vitt

Amblystegiaceae GRoth Anomodontaceae Kindb BrachytheciaceaeSchimp Calliergonaceae Vanderpoorten Hedenaumls CJCox amp AJShaw Catagoniaceae WRBuck amp Ireland Climaciaceae KindbCryphaeaceae Schimp Echinodiaceae Broth Entodontaceae KindbFabroniaceae Schimp Fontinalaceae Schimp Helodiaceae OchyraHeterocladiaceae Ignatov amp Ignatova Hylocomiaceae MFleischHypnaceae Schimp Lembophyllaceae Broth LeptodontaceaeSchimp Lepyrodontaceae Broth Leskeaceae Schimp Leucodon-taceae Schimp Meteoriaceae Kindb Microtheciellaceae HAMillamp AJHarr Myriniaceae Schimp Myuriaceae MFleisch NeckeraceaeSchimp Orthorrhynchiaceae SHLin Phyllogoniaceae KindbPlagiotheciaceae MFleisch Pleuroziopsidaceae Ireland Prionodon-taceae Broth Pseudoleskeaceae Schimp PseudoleskeellaceaeIgnatov amp Ignatova Pterigynandraceae Schimp PterobryaceaeKindb Pylaisiaceae Schimp Pylaisiadelphaceae Goffinet amp WRBuck Regmatodontaceae Broth Rhytidiaceae Broth RigodiaceaeHACrum Rutenbergiaceae MFleisch Scorpidiaceae Ignatov ampIgnatova Sematophyllaceae Broth Sorapillaceae MFleisch Ste-reophyllaceae WRBuck amp Ireland Symphyodontaceae MFleischTheliaceae MFleisch Thuidiaceae Schimp TrachylomataceaeWRBuck amp Vitt

Acknowledgements

Sincere thanks are due to JLReveal (Ithaca) as well as WFPrudhomme van Reine and JFVeldkamp(Leiden) for comments and discussions about suprafamilial taxonomy to DQuandt (Dresden) for providingDNA from Rhacocarpus and Bartramiaceae species and to BGiesicke (Berlin) for technical assistance

References

BECKERT S H MUHLE D PRUCHNER amp V KNOOP (2001) The mitochondrial nad2 geneas a novel marker locus for phylogenetic analysis of early land plants a comparative analysis inmosses - Mol Phylogenet Evol 18 117-126

BELL NE amp AE NEWTON (2004) Systematic studies of non-hypnanaean pleurocarps establishinga phylogenetic framework for investigating the origins of pleurocarpy - In GOFFINET BV HOLLOWELL amp R MAGILL (eds) Molecular systematics of bryophytes Monogr Syst BotMissouri Bot Gard 98 290-319

BELL NE amp AE NEWTON (2007) Pleurocarpy in the Rhizogoniaceous grade - In NEWTONAE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolution SystematicsAssociation Special Volume Series 71 41-64

BELL NE D QUANDT TJ OBRIEN amp AE NEWTON (2007) Taxonomy and phylogeny inthe earliest diverging pleurocarps square holes and bifurcating pegs - Bryologist 110 533-560

BORSCH T KW HILU D QUANDT V WILDE C NEINHUIS amp W BARTHLOTT(2003) Non-coding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms- J Evol Biol 16 558-576

18

BUCK WR (2007) The history of pleurocarp classification two steps forward one step back - InNEWTON AE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 1-18

BUCK WR amp B GOFFINET (2000) Morphology and classification of mosses - In SHAWAJ amp B GOFFINET (eds) Bryophyte Biology pp 71-123 Cambridge University PressCambridge

CHIANG TY BA SCHAAL amp CI PENG (1998) Universal primers for amplification andsequencing a noncoding spacer between atpB and rbcL genes of chloroplast DNA - Bot Bull AcadSin 39 245-250

COX CJ B GOFFINET AE NEWTON AJ SHAW amp TAJ HEDDERSON (2000)Phylogenetic relationships among the diplolepideous-alternate mosses (Bryidae) inferred from nuclearand chloroplast DNA sequences - Bryologist 103 224-241

COX CJ B GOFFINET AJ SHAW amp SB BOLES (2004) Phylogenetic relationships amongthe mosses based on heterogeneous Bayesian analysis of multiple genes from multiple genomiccompartments - Syst Bot 29 234-250

CRANDALL-STOTLER B (1986) Morphogenesis developmental anatomy and bryophytephylogenetics contra-indications of monophyly - J Bryol 14 1-23

CROSBY MR RE MAGILL B ALLEN amp S HE (1999) A checklist of the mosses - MissouriBotanical Garden St Louis Missouri

DOWELD A (2001) Prosyllabus Tracheophytorum - GEOS Moscow i-lxxx + 110 pp

DOYLE JJ amp JL DOYLE (1990) Isolation of plant DNA from fresh tissue - Focus 12 13-15

DUFF RJ JC VILLAREAL DC CARGILL amp KS RENZAGLIA (2007) Progress andchallenges towards developing a phylogeny and classification of the hornworts - Bryologist 110214-243

FLEISCHER M (1920) Natuumlrliches System der Laubmoose - Hedwigia 61 390-400

FORREST LL EC DAVIS DG LONG BJ CRANDALL-STOTLER A CLARK ampML HOLLINGSWORTH (2006) Unraveling the evolutionary history of the liverworts (Marchantio-phyta) multiple taxa genomes and analyses - Bryologist 109 303-334

FRAHM J-P amp W FREY (1987) Moosflora 2 Aufl - UTB 1250 Stuttgart

FREY W (1977) Neue Vorstellungen uumlber die Verwandtschaftsgruppen und die Stammesgeschichteder Laubmoose - In FREY W H HURKA amp F OBERWINKLER (Hrsg) Beitraumlge zur Biologieder Pflanzen pp 117-139 Stuttgart

FREY W amp M STECH (2005) A morpho-molecular classification of the liverworts (Hepa-ticophytina Bryophyta) - Nova Hedwigia 81 55-78

FREY W M STECH amp K MEIszligNER (1999) Chloroplast DNA-relationship in palaeoaustralLopidium concinnum (Hypopterygiaceae Musci) An example of steno-evolution in mosses Studiesin austral temperate rain forest bryophytes 2 - Plant Syst Evol 218 67-75

GOFFINET B amp WR BUCK (2004) Systematics of Bryophyta (mosses) from molecules to arevised classification - In GOFFINET B V HOLLOWELL amp R MAGILL (eds) Molecularsystematics of bryophytes Monogr Syst Bot Missouri Bot Gard 98 205-239

GOFFINET B CJ COX AJ SHAW amp TAJ HEDDERSON (2001) The Bryophyta (mosses)Systematic and evolutionary inferences from an rps4 gene (cpDNA) phylogeny - Ann Bot 87191-208

GOFFINET B NJ WICKETT O WERNER RM ROS AJ SHAW amp CJ COX (2007)Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae(Bryophyta) - Ann Bot 99 747-753

19

GROTH-MALONEK M D PRUCHNER F GREWE amp V KNOOP (2005) Ancestors oftrans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosseswith vascular plants - Mol Biol Evol 22 117-125

HATTORI S amp H INOUE (1958) Preliminary report on Takakia lepidozioides - J Hattori BotLab 19 133-137

HE-NYGREacuteN X A JUSLEacuteN I AHONEN D GLENNY amp S PIIPPO (2006) Illuminating theevolutionary history of liverworts (Marchantiophyta) - towards a natural classification - Cladistics22 1-31

HEDDERSON TAJ DJ MURRAY CJ COX amp TL NOWELL (2004) Phylogeneticrelationships of haplolepideous mosses (Dicranidae) inferred from rps4 gene sequences - Syst Bot29 29-41

LA FARGE C BD MISHER JA WHEELER DP WALL K JOHANNES S SCHAFFERamp AJ SHAW (2000) Phylogenetic relationships within the haplolepideous mosses - Bryologist103 257-276

LA FARGE C AJ SHAW amp DH VITT (2002) The circumscription of the Dicranaceae(Bryopsida) based on the chloroplast regions trnL-trnF and rps4 - Syst Bot 27 435-452

MAGOMBO ZLK (2003) The phylogeny of basal peristomate mosses evidence from cpDNAand implications for peristome evolution - Syst Bot 28 24-38

MCNEILL J FR BARRIE HM BURDET V DEMOULIN DL HAWKSWORTHK MARHOLD DH NICOLSON J PRADO PC SILVA JE SKOG JH WIERSEMA ampNJ TURLAND (2006) International Code of Botanical Nomenclature (Vienna Code) - RegnumVegetabile 146 1-568

MUumlLLER K (2004) PRAP - computation of Bremer support for large data sets - Mol PhylogenetEvol 31 780-782

MUumlLLER K (2005) SeqState - primer design and sequence statistics for phylogenetic DNA datasets - Appl Bioinformatics 4 65-69

MUumlLLER K D QUANDT J MUumlLLER amp C NEINHUIS (2005) PhyDE v0992 PhylogeneticData Editor - httpwwwphydede

MURRAY BM (1988) Systematics of the Andreaeopsida (Bryophyta) two orders with links toTakakia - Nova Hedwigia Beih 90 289-336

NEWTON AE amp RS TANGNEY (eds) (2007) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 CRC Press Boca Raton 434 pp

NEWTON AE CJ COX JG DUCKETT JA WHEELER B GOFFINET TAJ HEDDER-SON amp BD MISHLER (2000) Evolution of the major moss lineages Phylogenetic analyses basedon multiple gene sequences and morphology - Bryologist 103 187-211

NEWTON AE N WIKSTROumlM NE BELL LL FORREST amp MS IGNATOV (2007)Dating the diversification of the pleurocarpous mosses - In NEWTON AE amp RS TANGNEY(eds) Pleurocarpous mosses systematics and evolution Systematics Association Special VolumeSeries 71 337-366

NIXON KC (1999) The parsimony ratchet a new method for rapid parsimony analysis - Cladistics15 407-411

OBRIEN TJ (2007) The phylogenetic distribution of pleurocarpous mosses evidence fromcpDNA sequences - In NEWTON AE amp RS TANGNEY (eds) Pleurocarpous mossessystematics and evolution Systematics Association Special Volume Series 71 19-41

OCHYRA R (2002) Nomenclatural changes in subfamilies of the Dicranaceae - CryptogamieBryol 23 345-349

20

OCHYRA R J ŻARNOWIEC amp H BEDNAREK-OCHYRA (2003) Census catalogue ofPolish mosses - Biodiv Poland 3 1-372

PEDERSEN N amp AE NEWTON (2007) Phylogenetic and morphological studies within thePtychomniales with emphasis on the evolution of dwarf males - In NEWTON AE amp RSTANGNEY (eds) Pleurocarpous mosses systematics and evolution Systematics AssociationSpecial Volume Series 71 367-392

QUANDT D amp M STECH (2005) Molecular evolution and secondary structure of the chloroplasttrnL intron in bryophytes - Mol Phylogenet Evol 36 429-443

QUANDT D K MUumlLLER amp S HUTTUNEN (2003) Characterisation of the chloroplast DNApsbT-H region and the influence of dyad symmetrical elements on phylogenetic reconstructions -Plant Biol 5 400-410

QUANDT D K MUumlLLER M STECH W FREY KW HILU amp T BORSCH (2004) Molecularevolution of the chloroplast trnL-F-region in land plants - In GOFFINET B V HOLLOWELL ampR MAGILL (eds) Molecular systematics of bryophytes Monogr Syst Bot Missouri Bot Gard98 13-37

QUANDT D NE BELL amp M STECH (2007) Unravelling the knot the Pulchrinodaceae famnov (Bryales) - In KUumlRSCHNER H T PFEIFFER amp M STECH (eds) A Festschrift to Wolf-gang Frey - a scientists life between deserts and rain forests Nova Hedwigia Beih 131 21-39

QIU Y-L Y CHO JC COX amp JD PALMER (1998) The gain of three mitochondrial intronsidentifies liverworts as the earliest land plants - Nature 394 671-674

QIU Y-L L LI B WANG Z CHEN V KNOOP M GROTH-MALONEK O DOM-BROVSKA J LEE L KENT J REST GF ESTABROOK TA HENDRY DW TAYLORCM TESTA M AMBROS B CRANDALL-STOTLER J DUFF M STECH W FREYD QUANDT amp CC DAVIS (2006) The deepest divergences in land plants inferred fromphylogenomic evidence - Proc Natl Acad Sci USA 103 15511-15516

RENZAGLIA KS S SCHUETTE RJ DUFF R LIGRONE AJ SHAW BD MISHLER ampJG DUCKETT (2007) Bryophyte phylogeny Advancing the molecular and morphological frontiers- Bryologist 110 179-213

SAMIGULLIN TH SP YACENTYUK GV DEGTYARYEVA KM VALIEJO-ROMANVK BOBROVA I CAPESIUS WF MARTIN AV TROITSKY VR FILIN amp ASANTONOV (2002) Paraphyly of bryophytes and close relationships of hornworts and vascularplants inferred from analysis of chloroplast rDNA ITS (cpITS) sequences - Arctoa 11 31-43

SANG T DJ CRAWFORD amp TF STUESSY (1997) Chloroplast DNA phylogeny reticulateevolution and biogeography of Paeonia (Paeoniaceae) - Amer J Bot 84 1120-1136

SHAW AJ amp KS RENZAGLIA (2004) Phylogeny and diversification of bryophytes - AmerJ Bot 91 1557-1581

SHAW AJ CJ COX amp B GOFFINET (2005) Global patterns of moss diversity taxonomic andmolecular inferences - Taxon 54 337-352

STECH M (1999a) A reclassification of Dicranaceae (Bryopsida) based on non-coding cpDNAsequence data - J Hattori Bot Lab 86 137-159

STECH M (1999b) A molecular systematic contribution to the position of Amphidium Schimp(Rhabdoweisiaceae Bryopsida) - Nova Hedwigia 68 291-300

STECH M (2004) Supraspecific circumscription and classification of Campylopus Brid(Dicranaceae Bryopsida) based on molecular data - Syst Bot 29 817-824

STECH M amp D QUANDT (2006) Molecular evolution of the chloroplast atpB-rbcL spacer inbryophytes - In SHARMA AK amp A SHARMA (eds) Plant Genome Biodiversity and EvolutionVol 2 Part B pp 409-431 Science Publishers Enfield New Hampshire

21

STECH M D QUANDT amp W FREY (2003) Molecular circumscription of the hornworts(Antho-cerotophyta) based on the chloroplast DNA trnL-trnF region - J Plant Res 116 389-398

STOTLER RE amp B CRANDALL-STOTLER (2005) A revised classification of theAnthocerotophyta and a checklist of the hornworts of North America north of Mexico - Bryologist108 16-26

SWOFFORD DL (2002) PAUP Phylogenetic analysis using parsimony (and other methods)version 40b10 - Sunderland MA

TABERLET P L GIELLY G PAUTOU amp J BOUVET (1991) Universal primers for amplificationof three non-coding regions of chloroplast DNA - Plant Mol Biol 17 1105-1109

TSUBOTA H Y AGENO B ESTEacuteBANEZ T YAMAGUCHI amp H DEGUCHI (2003)Molecular phylogeny of the Grimmiales (Musci) based on chloroplast rbcL sequences - Hikobia 1455-70

TSUBOTA H E DE LUNA D GONZAacuteLEZ MS IGNATOV amp H DEGUCHI (2004) Molecularphylogenetics and ordinal relationships based on analyses of a large-scale data set of 600 rbcLsequences of mosses - Hikobia 14 149-170

VITT DH (1984) Classification of the Bryopsida - In SCHUSTER RM (ed) New Manual ofBryology 2 696-759 Hattori Botanical Laboratory Nichinan Japan

VITT DH B GOFFINET amp T HEDDERSON (1998) 8 The ordinal classification of the mossesquestions and answers for the 1990s - In BATES JW NW ASHTON amp JG DUCKETT (eds)Bryology for the twenty-first century British Bryol Soc pp 113-123

Received 3 September 2007 accepted in revised form 30 October 2007

Page 14: botanica parcial 3

14

TYPUS Gigaspermum Lindb Oumlfversigt af Foumlrhandlingar Kongl Svenska Vetenskaps-Akademien21 599 1865

Amphidiaceae Stech stat nov

Based on Dicranaceae subfam Amphidioideae Ochyra in Ochyra Zarnowiec amp Bednarek-OchyraCens Cat Polish Mosses 110 2003

TYPUS Amphidium Schimp Coroll Bryol Eur 39 1856

Amphidiaceae AJESm Moss Fl Britain Ireland 2nd ed 657 2004 nom inval descr angl

Dicranellaceae Stech stat nov

Based on Dicranaceae subfam Dicranelloideae Lindb Utkast Eur Bladmoss 33 1878[lsquoUnderfamilje Dicranelleaersquo]

TYPUS Dicranella (MuumlllHal) Schimp Coroll Bryol Eur 13 1856

Oncophoraceae Stech stat nov

Based on Dicranaceae subfam Oncophoroideae Lindb Utkast Eur Bladmoss 34 1878[lsquoUnderfamilje Oncophoreaersquo]

TYPUS Oncophorus (Brid) Brid Bryol Univ 1 389 1826

Hypodontiaceae Stech fam nov

Plantae robustae characteribus morphologicis Pottiaceis et Calymperaceis similes sedcharacteribus molecularicis separatae Bracteae perichaetiales internae e basi vaginantes subulataevel aristatae Capsula aspectu succulenta cellulae exothecii incrassatae annulus magnopereabsens Peristomii dentes breves triangulati incurvati aurantiaci leves vel infirme verrucosiCalyptra cucullata

TYPUS Hypodontium MuumlllHal Hedwigia 38 96 1899

Helicophyllales Stech amp WFrey ord nov

Plantae acrocarpae prostratae tomentosae Folia dimorpha in duas series laterales et unam seriemventralem divisa Costa percurrens Cellulae hexagonae ad subquadratae papillosae Capsula immersacupulata ad oblonga infra orificium abrupte incurvata stomata destituta Peristomium nullum Sporaeisomorphae heteropolares granulatae

TYPUS Helicophyllum Brid Bryol Univ 2 771 1827

Synopsis of the suprageneric classification of BryophytaAuthor citations are in accordance with Art 492 of the Vienna Code (McNeill et al 2006)

Subdivision Takakiophytina Stech amp WFreyClass Takakiopsida Stech amp WFrey

Order Takakiales Stech amp WFreyTakakiaceae Stech amp WFrey

Subdivision Sphagnophytina DoweldClass Sphagnopsida Schimp

Order Sphagnales Limpr

15

Sphagnaceae DumortOrder Ambuchananiales Seppelt amp HACrum

Ambuchananiaceae Seppelt amp HACrumSubdivision Bryophytina Engler

Class Andreaeopsida JHSchaffnSubclass Andreaeidae Engl

Order Andreaeales LimprAndreaeaceae Dumort

Subclass Andreaeobryidae OchyraOrder Andreaeobryales BMMurray

Andreaeobryaceae Steere amp BMMurrayClass Oedipodiopsida Goffinet amp WRBuck

Order Oedipodiales Goffinet amp WRBuckOedipodiaceae Schimp

Class Tetraphidopsida Goffinet amp WRBuckOrder Tetraphidales MFleisch

Tetraphidaceae SchimpClass Polytrichopsida Doweld

Order Polytrichales MFleischPolytrichaceae Schwaumlgr

Class Bryopsida PaxSubclass Buxbaumiidae Doweld

Order Buxbaumiales MFleischBuxbaumiaceae Schimp

Subclass Diphysciidae OchyraOrder Diphysciales MFleisch

Diphysciaceae MFleischSubclass Timmiidae Ochyra

Order Timmiales OchyraTimmiaceae Schimp

Subclass Encalyptidae Ochyra Żarnowiec amp Bednarek-OchyraOrder Encalyptales Dixon

Encalyptaceae SchimpSubclass Funariidae Ochyra

Order Funariales MFleischFunariaceae Schwaumlgr Disceliaceae Schimp

Subclass Gigaspermidae Stech amp WFreyOrder Gigaspermales Goffinet Wickett OWerner Ros AJShaw amp CJCox

Gigaspermaceae LindbSubclass Dicranidae Doweld

Order Catoscopiales Ignatov amp IgnatovaCatoscopiaceae Broth

Order Scouleriales Goffinet amp WRBuckDrummondiaceae Goffinet Scouleriaceae SPChurchill

Order Bryoxiphiales HACrum amp LEAndersonBryoxiphiaceae Besch

16

Order Grimmiales MFleischGrimmiaceae Arn Ptychomitriaceae Schimp Seligeriaceae Schimp

Order Archidiales LimprArchidiaceae Schimp

Order Mitteniales ShawMitteniaceae Broth

Order Dicranales HPhilib ex MFleischAmphidiaceae Stech Aongstroemiaceae De Not BruchiaceaeSchimp Calymperaceae Kindb Dicranaceae Schimp Dicranel-laceae Stech Ditrichaceae Limpr Erpodiaceae Broth EustichiaceaeBroth Fissidentaceae Schimp Leucobryaceae Schimp Onco-phoraceae Stech Rhachitheciaceae HRob Schistostegaceae SchimpViridivelleraceae IGStone Wardiaceae Welch

Order Pottiales MFleischEphemeraceae Schimp Hypodontiaceae Stech PleurophascaceaeBroth Pottiaceae Schimp Serpotortellaceae WDReese amp RHZander

Subclass Bryidae EnglOrder Hedwigiales Ochyra

Hedwigiaceae Schimp Rhacocarpaceae KindbOrder Helicophyllales Stech amp WFrey

Helicophyllaceae BrothOrder Bartramiales DQuandt NEBell amp Stech

Bartramiaceae SchwaumlgrOrder Splachnales Ochyra

Meesiaceae Schimp Splachnaceae Grev amp ArnOrder Bryales Limpr

Bryaceae Schwaumlgr Leptostomataceae Schwaumlgr Mniaceae SchwaumlgrPhyllodrepaniaceae Crosby Pseudoditrichaceae Steere amp ZIwatsPulchrinodaceae DQuandt NEBell amp Stech

Order Orthotrichales DixonOrthotrichaceae Arn

Order Orthodontiales NEBell AENewton amp DQuandtOrthodontiaceae Goffinet

Order Aulacomniales NEBell AENewton amp DQuandtAulacomniaceae Schimp

Order Rhizogoniales Goffinet amp WRBuckRhizogoniaceae Broth

Order Hypnodendrales NEBell AENewton amp DQuandtBraithwaiteaceae NEBell AENewton amp DQuandt Hypnodendra-ceae Broth Pterobryellaceae WRBuck amp Vitt Racopilaceae Kindb

Order Ptychomniales WRBuck CJCox AJShaw amp GoffinetPtychomniaceae MFleisch

Order Hookeriales MFleischDaltoniaceae Schimp Hookeriaceae Schimp HypopterygiaceaeMitt Leucomiaceae Broth Pilotrichaceae Kindb SaulomataceaeWRBuck CJCox AJShaw amp Goffinet Schimperobryaceae WR

17

Buck CJCox AJShaw amp GoffinetOrder Hypnales WRBuck amp Vitt

Amblystegiaceae GRoth Anomodontaceae Kindb BrachytheciaceaeSchimp Calliergonaceae Vanderpoorten Hedenaumls CJCox amp AJShaw Catagoniaceae WRBuck amp Ireland Climaciaceae KindbCryphaeaceae Schimp Echinodiaceae Broth Entodontaceae KindbFabroniaceae Schimp Fontinalaceae Schimp Helodiaceae OchyraHeterocladiaceae Ignatov amp Ignatova Hylocomiaceae MFleischHypnaceae Schimp Lembophyllaceae Broth LeptodontaceaeSchimp Lepyrodontaceae Broth Leskeaceae Schimp Leucodon-taceae Schimp Meteoriaceae Kindb Microtheciellaceae HAMillamp AJHarr Myriniaceae Schimp Myuriaceae MFleisch NeckeraceaeSchimp Orthorrhynchiaceae SHLin Phyllogoniaceae KindbPlagiotheciaceae MFleisch Pleuroziopsidaceae Ireland Prionodon-taceae Broth Pseudoleskeaceae Schimp PseudoleskeellaceaeIgnatov amp Ignatova Pterigynandraceae Schimp PterobryaceaeKindb Pylaisiaceae Schimp Pylaisiadelphaceae Goffinet amp WRBuck Regmatodontaceae Broth Rhytidiaceae Broth RigodiaceaeHACrum Rutenbergiaceae MFleisch Scorpidiaceae Ignatov ampIgnatova Sematophyllaceae Broth Sorapillaceae MFleisch Ste-reophyllaceae WRBuck amp Ireland Symphyodontaceae MFleischTheliaceae MFleisch Thuidiaceae Schimp TrachylomataceaeWRBuck amp Vitt

Acknowledgements

Sincere thanks are due to JLReveal (Ithaca) as well as WFPrudhomme van Reine and JFVeldkamp(Leiden) for comments and discussions about suprafamilial taxonomy to DQuandt (Dresden) for providingDNA from Rhacocarpus and Bartramiaceae species and to BGiesicke (Berlin) for technical assistance

References

BECKERT S H MUHLE D PRUCHNER amp V KNOOP (2001) The mitochondrial nad2 geneas a novel marker locus for phylogenetic analysis of early land plants a comparative analysis inmosses - Mol Phylogenet Evol 18 117-126

BELL NE amp AE NEWTON (2004) Systematic studies of non-hypnanaean pleurocarps establishinga phylogenetic framework for investigating the origins of pleurocarpy - In GOFFINET BV HOLLOWELL amp R MAGILL (eds) Molecular systematics of bryophytes Monogr Syst BotMissouri Bot Gard 98 290-319

BELL NE amp AE NEWTON (2007) Pleurocarpy in the Rhizogoniaceous grade - In NEWTONAE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolution SystematicsAssociation Special Volume Series 71 41-64

BELL NE D QUANDT TJ OBRIEN amp AE NEWTON (2007) Taxonomy and phylogeny inthe earliest diverging pleurocarps square holes and bifurcating pegs - Bryologist 110 533-560

BORSCH T KW HILU D QUANDT V WILDE C NEINHUIS amp W BARTHLOTT(2003) Non-coding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms- J Evol Biol 16 558-576

18

BUCK WR (2007) The history of pleurocarp classification two steps forward one step back - InNEWTON AE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 1-18

BUCK WR amp B GOFFINET (2000) Morphology and classification of mosses - In SHAWAJ amp B GOFFINET (eds) Bryophyte Biology pp 71-123 Cambridge University PressCambridge

CHIANG TY BA SCHAAL amp CI PENG (1998) Universal primers for amplification andsequencing a noncoding spacer between atpB and rbcL genes of chloroplast DNA - Bot Bull AcadSin 39 245-250

COX CJ B GOFFINET AE NEWTON AJ SHAW amp TAJ HEDDERSON (2000)Phylogenetic relationships among the diplolepideous-alternate mosses (Bryidae) inferred from nuclearand chloroplast DNA sequences - Bryologist 103 224-241

COX CJ B GOFFINET AJ SHAW amp SB BOLES (2004) Phylogenetic relationships amongthe mosses based on heterogeneous Bayesian analysis of multiple genes from multiple genomiccompartments - Syst Bot 29 234-250

CRANDALL-STOTLER B (1986) Morphogenesis developmental anatomy and bryophytephylogenetics contra-indications of monophyly - J Bryol 14 1-23

CROSBY MR RE MAGILL B ALLEN amp S HE (1999) A checklist of the mosses - MissouriBotanical Garden St Louis Missouri

DOWELD A (2001) Prosyllabus Tracheophytorum - GEOS Moscow i-lxxx + 110 pp

DOYLE JJ amp JL DOYLE (1990) Isolation of plant DNA from fresh tissue - Focus 12 13-15

DUFF RJ JC VILLAREAL DC CARGILL amp KS RENZAGLIA (2007) Progress andchallenges towards developing a phylogeny and classification of the hornworts - Bryologist 110214-243

FLEISCHER M (1920) Natuumlrliches System der Laubmoose - Hedwigia 61 390-400

FORREST LL EC DAVIS DG LONG BJ CRANDALL-STOTLER A CLARK ampML HOLLINGSWORTH (2006) Unraveling the evolutionary history of the liverworts (Marchantio-phyta) multiple taxa genomes and analyses - Bryologist 109 303-334

FRAHM J-P amp W FREY (1987) Moosflora 2 Aufl - UTB 1250 Stuttgart

FREY W (1977) Neue Vorstellungen uumlber die Verwandtschaftsgruppen und die Stammesgeschichteder Laubmoose - In FREY W H HURKA amp F OBERWINKLER (Hrsg) Beitraumlge zur Biologieder Pflanzen pp 117-139 Stuttgart

FREY W amp M STECH (2005) A morpho-molecular classification of the liverworts (Hepa-ticophytina Bryophyta) - Nova Hedwigia 81 55-78

FREY W M STECH amp K MEIszligNER (1999) Chloroplast DNA-relationship in palaeoaustralLopidium concinnum (Hypopterygiaceae Musci) An example of steno-evolution in mosses Studiesin austral temperate rain forest bryophytes 2 - Plant Syst Evol 218 67-75

GOFFINET B amp WR BUCK (2004) Systematics of Bryophyta (mosses) from molecules to arevised classification - In GOFFINET B V HOLLOWELL amp R MAGILL (eds) Molecularsystematics of bryophytes Monogr Syst Bot Missouri Bot Gard 98 205-239

GOFFINET B CJ COX AJ SHAW amp TAJ HEDDERSON (2001) The Bryophyta (mosses)Systematic and evolutionary inferences from an rps4 gene (cpDNA) phylogeny - Ann Bot 87191-208

GOFFINET B NJ WICKETT O WERNER RM ROS AJ SHAW amp CJ COX (2007)Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae(Bryophyta) - Ann Bot 99 747-753

19

GROTH-MALONEK M D PRUCHNER F GREWE amp V KNOOP (2005) Ancestors oftrans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosseswith vascular plants - Mol Biol Evol 22 117-125

HATTORI S amp H INOUE (1958) Preliminary report on Takakia lepidozioides - J Hattori BotLab 19 133-137

HE-NYGREacuteN X A JUSLEacuteN I AHONEN D GLENNY amp S PIIPPO (2006) Illuminating theevolutionary history of liverworts (Marchantiophyta) - towards a natural classification - Cladistics22 1-31

HEDDERSON TAJ DJ MURRAY CJ COX amp TL NOWELL (2004) Phylogeneticrelationships of haplolepideous mosses (Dicranidae) inferred from rps4 gene sequences - Syst Bot29 29-41

LA FARGE C BD MISHER JA WHEELER DP WALL K JOHANNES S SCHAFFERamp AJ SHAW (2000) Phylogenetic relationships within the haplolepideous mosses - Bryologist103 257-276

LA FARGE C AJ SHAW amp DH VITT (2002) The circumscription of the Dicranaceae(Bryopsida) based on the chloroplast regions trnL-trnF and rps4 - Syst Bot 27 435-452

MAGOMBO ZLK (2003) The phylogeny of basal peristomate mosses evidence from cpDNAand implications for peristome evolution - Syst Bot 28 24-38

MCNEILL J FR BARRIE HM BURDET V DEMOULIN DL HAWKSWORTHK MARHOLD DH NICOLSON J PRADO PC SILVA JE SKOG JH WIERSEMA ampNJ TURLAND (2006) International Code of Botanical Nomenclature (Vienna Code) - RegnumVegetabile 146 1-568

MUumlLLER K (2004) PRAP - computation of Bremer support for large data sets - Mol PhylogenetEvol 31 780-782

MUumlLLER K (2005) SeqState - primer design and sequence statistics for phylogenetic DNA datasets - Appl Bioinformatics 4 65-69

MUumlLLER K D QUANDT J MUumlLLER amp C NEINHUIS (2005) PhyDE v0992 PhylogeneticData Editor - httpwwwphydede

MURRAY BM (1988) Systematics of the Andreaeopsida (Bryophyta) two orders with links toTakakia - Nova Hedwigia Beih 90 289-336

NEWTON AE amp RS TANGNEY (eds) (2007) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 CRC Press Boca Raton 434 pp

NEWTON AE CJ COX JG DUCKETT JA WHEELER B GOFFINET TAJ HEDDER-SON amp BD MISHLER (2000) Evolution of the major moss lineages Phylogenetic analyses basedon multiple gene sequences and morphology - Bryologist 103 187-211

NEWTON AE N WIKSTROumlM NE BELL LL FORREST amp MS IGNATOV (2007)Dating the diversification of the pleurocarpous mosses - In NEWTON AE amp RS TANGNEY(eds) Pleurocarpous mosses systematics and evolution Systematics Association Special VolumeSeries 71 337-366

NIXON KC (1999) The parsimony ratchet a new method for rapid parsimony analysis - Cladistics15 407-411

OBRIEN TJ (2007) The phylogenetic distribution of pleurocarpous mosses evidence fromcpDNA sequences - In NEWTON AE amp RS TANGNEY (eds) Pleurocarpous mossessystematics and evolution Systematics Association Special Volume Series 71 19-41

OCHYRA R (2002) Nomenclatural changes in subfamilies of the Dicranaceae - CryptogamieBryol 23 345-349

20

OCHYRA R J ŻARNOWIEC amp H BEDNAREK-OCHYRA (2003) Census catalogue ofPolish mosses - Biodiv Poland 3 1-372

PEDERSEN N amp AE NEWTON (2007) Phylogenetic and morphological studies within thePtychomniales with emphasis on the evolution of dwarf males - In NEWTON AE amp RSTANGNEY (eds) Pleurocarpous mosses systematics and evolution Systematics AssociationSpecial Volume Series 71 367-392

QUANDT D amp M STECH (2005) Molecular evolution and secondary structure of the chloroplasttrnL intron in bryophytes - Mol Phylogenet Evol 36 429-443

QUANDT D K MUumlLLER amp S HUTTUNEN (2003) Characterisation of the chloroplast DNApsbT-H region and the influence of dyad symmetrical elements on phylogenetic reconstructions -Plant Biol 5 400-410

QUANDT D K MUumlLLER M STECH W FREY KW HILU amp T BORSCH (2004) Molecularevolution of the chloroplast trnL-F-region in land plants - In GOFFINET B V HOLLOWELL ampR MAGILL (eds) Molecular systematics of bryophytes Monogr Syst Bot Missouri Bot Gard98 13-37

QUANDT D NE BELL amp M STECH (2007) Unravelling the knot the Pulchrinodaceae famnov (Bryales) - In KUumlRSCHNER H T PFEIFFER amp M STECH (eds) A Festschrift to Wolf-gang Frey - a scientists life between deserts and rain forests Nova Hedwigia Beih 131 21-39

QIU Y-L Y CHO JC COX amp JD PALMER (1998) The gain of three mitochondrial intronsidentifies liverworts as the earliest land plants - Nature 394 671-674

QIU Y-L L LI B WANG Z CHEN V KNOOP M GROTH-MALONEK O DOM-BROVSKA J LEE L KENT J REST GF ESTABROOK TA HENDRY DW TAYLORCM TESTA M AMBROS B CRANDALL-STOTLER J DUFF M STECH W FREYD QUANDT amp CC DAVIS (2006) The deepest divergences in land plants inferred fromphylogenomic evidence - Proc Natl Acad Sci USA 103 15511-15516

RENZAGLIA KS S SCHUETTE RJ DUFF R LIGRONE AJ SHAW BD MISHLER ampJG DUCKETT (2007) Bryophyte phylogeny Advancing the molecular and morphological frontiers- Bryologist 110 179-213

SAMIGULLIN TH SP YACENTYUK GV DEGTYARYEVA KM VALIEJO-ROMANVK BOBROVA I CAPESIUS WF MARTIN AV TROITSKY VR FILIN amp ASANTONOV (2002) Paraphyly of bryophytes and close relationships of hornworts and vascularplants inferred from analysis of chloroplast rDNA ITS (cpITS) sequences - Arctoa 11 31-43

SANG T DJ CRAWFORD amp TF STUESSY (1997) Chloroplast DNA phylogeny reticulateevolution and biogeography of Paeonia (Paeoniaceae) - Amer J Bot 84 1120-1136

SHAW AJ amp KS RENZAGLIA (2004) Phylogeny and diversification of bryophytes - AmerJ Bot 91 1557-1581

SHAW AJ CJ COX amp B GOFFINET (2005) Global patterns of moss diversity taxonomic andmolecular inferences - Taxon 54 337-352

STECH M (1999a) A reclassification of Dicranaceae (Bryopsida) based on non-coding cpDNAsequence data - J Hattori Bot Lab 86 137-159

STECH M (1999b) A molecular systematic contribution to the position of Amphidium Schimp(Rhabdoweisiaceae Bryopsida) - Nova Hedwigia 68 291-300

STECH M (2004) Supraspecific circumscription and classification of Campylopus Brid(Dicranaceae Bryopsida) based on molecular data - Syst Bot 29 817-824

STECH M amp D QUANDT (2006) Molecular evolution of the chloroplast atpB-rbcL spacer inbryophytes - In SHARMA AK amp A SHARMA (eds) Plant Genome Biodiversity and EvolutionVol 2 Part B pp 409-431 Science Publishers Enfield New Hampshire

21

STECH M D QUANDT amp W FREY (2003) Molecular circumscription of the hornworts(Antho-cerotophyta) based on the chloroplast DNA trnL-trnF region - J Plant Res 116 389-398

STOTLER RE amp B CRANDALL-STOTLER (2005) A revised classification of theAnthocerotophyta and a checklist of the hornworts of North America north of Mexico - Bryologist108 16-26

SWOFFORD DL (2002) PAUP Phylogenetic analysis using parsimony (and other methods)version 40b10 - Sunderland MA

TABERLET P L GIELLY G PAUTOU amp J BOUVET (1991) Universal primers for amplificationof three non-coding regions of chloroplast DNA - Plant Mol Biol 17 1105-1109

TSUBOTA H Y AGENO B ESTEacuteBANEZ T YAMAGUCHI amp H DEGUCHI (2003)Molecular phylogeny of the Grimmiales (Musci) based on chloroplast rbcL sequences - Hikobia 1455-70

TSUBOTA H E DE LUNA D GONZAacuteLEZ MS IGNATOV amp H DEGUCHI (2004) Molecularphylogenetics and ordinal relationships based on analyses of a large-scale data set of 600 rbcLsequences of mosses - Hikobia 14 149-170

VITT DH (1984) Classification of the Bryopsida - In SCHUSTER RM (ed) New Manual ofBryology 2 696-759 Hattori Botanical Laboratory Nichinan Japan

VITT DH B GOFFINET amp T HEDDERSON (1998) 8 The ordinal classification of the mossesquestions and answers for the 1990s - In BATES JW NW ASHTON amp JG DUCKETT (eds)Bryology for the twenty-first century British Bryol Soc pp 113-123

Received 3 September 2007 accepted in revised form 30 October 2007

Page 15: botanica parcial 3

15

Sphagnaceae DumortOrder Ambuchananiales Seppelt amp HACrum

Ambuchananiaceae Seppelt amp HACrumSubdivision Bryophytina Engler

Class Andreaeopsida JHSchaffnSubclass Andreaeidae Engl

Order Andreaeales LimprAndreaeaceae Dumort

Subclass Andreaeobryidae OchyraOrder Andreaeobryales BMMurray

Andreaeobryaceae Steere amp BMMurrayClass Oedipodiopsida Goffinet amp WRBuck

Order Oedipodiales Goffinet amp WRBuckOedipodiaceae Schimp

Class Tetraphidopsida Goffinet amp WRBuckOrder Tetraphidales MFleisch

Tetraphidaceae SchimpClass Polytrichopsida Doweld

Order Polytrichales MFleischPolytrichaceae Schwaumlgr

Class Bryopsida PaxSubclass Buxbaumiidae Doweld

Order Buxbaumiales MFleischBuxbaumiaceae Schimp

Subclass Diphysciidae OchyraOrder Diphysciales MFleisch

Diphysciaceae MFleischSubclass Timmiidae Ochyra

Order Timmiales OchyraTimmiaceae Schimp

Subclass Encalyptidae Ochyra Żarnowiec amp Bednarek-OchyraOrder Encalyptales Dixon

Encalyptaceae SchimpSubclass Funariidae Ochyra

Order Funariales MFleischFunariaceae Schwaumlgr Disceliaceae Schimp

Subclass Gigaspermidae Stech amp WFreyOrder Gigaspermales Goffinet Wickett OWerner Ros AJShaw amp CJCox

Gigaspermaceae LindbSubclass Dicranidae Doweld

Order Catoscopiales Ignatov amp IgnatovaCatoscopiaceae Broth

Order Scouleriales Goffinet amp WRBuckDrummondiaceae Goffinet Scouleriaceae SPChurchill

Order Bryoxiphiales HACrum amp LEAndersonBryoxiphiaceae Besch

16

Order Grimmiales MFleischGrimmiaceae Arn Ptychomitriaceae Schimp Seligeriaceae Schimp

Order Archidiales LimprArchidiaceae Schimp

Order Mitteniales ShawMitteniaceae Broth

Order Dicranales HPhilib ex MFleischAmphidiaceae Stech Aongstroemiaceae De Not BruchiaceaeSchimp Calymperaceae Kindb Dicranaceae Schimp Dicranel-laceae Stech Ditrichaceae Limpr Erpodiaceae Broth EustichiaceaeBroth Fissidentaceae Schimp Leucobryaceae Schimp Onco-phoraceae Stech Rhachitheciaceae HRob Schistostegaceae SchimpViridivelleraceae IGStone Wardiaceae Welch

Order Pottiales MFleischEphemeraceae Schimp Hypodontiaceae Stech PleurophascaceaeBroth Pottiaceae Schimp Serpotortellaceae WDReese amp RHZander

Subclass Bryidae EnglOrder Hedwigiales Ochyra

Hedwigiaceae Schimp Rhacocarpaceae KindbOrder Helicophyllales Stech amp WFrey

Helicophyllaceae BrothOrder Bartramiales DQuandt NEBell amp Stech

Bartramiaceae SchwaumlgrOrder Splachnales Ochyra

Meesiaceae Schimp Splachnaceae Grev amp ArnOrder Bryales Limpr

Bryaceae Schwaumlgr Leptostomataceae Schwaumlgr Mniaceae SchwaumlgrPhyllodrepaniaceae Crosby Pseudoditrichaceae Steere amp ZIwatsPulchrinodaceae DQuandt NEBell amp Stech

Order Orthotrichales DixonOrthotrichaceae Arn

Order Orthodontiales NEBell AENewton amp DQuandtOrthodontiaceae Goffinet

Order Aulacomniales NEBell AENewton amp DQuandtAulacomniaceae Schimp

Order Rhizogoniales Goffinet amp WRBuckRhizogoniaceae Broth

Order Hypnodendrales NEBell AENewton amp DQuandtBraithwaiteaceae NEBell AENewton amp DQuandt Hypnodendra-ceae Broth Pterobryellaceae WRBuck amp Vitt Racopilaceae Kindb

Order Ptychomniales WRBuck CJCox AJShaw amp GoffinetPtychomniaceae MFleisch

Order Hookeriales MFleischDaltoniaceae Schimp Hookeriaceae Schimp HypopterygiaceaeMitt Leucomiaceae Broth Pilotrichaceae Kindb SaulomataceaeWRBuck CJCox AJShaw amp Goffinet Schimperobryaceae WR

17

Buck CJCox AJShaw amp GoffinetOrder Hypnales WRBuck amp Vitt

Amblystegiaceae GRoth Anomodontaceae Kindb BrachytheciaceaeSchimp Calliergonaceae Vanderpoorten Hedenaumls CJCox amp AJShaw Catagoniaceae WRBuck amp Ireland Climaciaceae KindbCryphaeaceae Schimp Echinodiaceae Broth Entodontaceae KindbFabroniaceae Schimp Fontinalaceae Schimp Helodiaceae OchyraHeterocladiaceae Ignatov amp Ignatova Hylocomiaceae MFleischHypnaceae Schimp Lembophyllaceae Broth LeptodontaceaeSchimp Lepyrodontaceae Broth Leskeaceae Schimp Leucodon-taceae Schimp Meteoriaceae Kindb Microtheciellaceae HAMillamp AJHarr Myriniaceae Schimp Myuriaceae MFleisch NeckeraceaeSchimp Orthorrhynchiaceae SHLin Phyllogoniaceae KindbPlagiotheciaceae MFleisch Pleuroziopsidaceae Ireland Prionodon-taceae Broth Pseudoleskeaceae Schimp PseudoleskeellaceaeIgnatov amp Ignatova Pterigynandraceae Schimp PterobryaceaeKindb Pylaisiaceae Schimp Pylaisiadelphaceae Goffinet amp WRBuck Regmatodontaceae Broth Rhytidiaceae Broth RigodiaceaeHACrum Rutenbergiaceae MFleisch Scorpidiaceae Ignatov ampIgnatova Sematophyllaceae Broth Sorapillaceae MFleisch Ste-reophyllaceae WRBuck amp Ireland Symphyodontaceae MFleischTheliaceae MFleisch Thuidiaceae Schimp TrachylomataceaeWRBuck amp Vitt

Acknowledgements

Sincere thanks are due to JLReveal (Ithaca) as well as WFPrudhomme van Reine and JFVeldkamp(Leiden) for comments and discussions about suprafamilial taxonomy to DQuandt (Dresden) for providingDNA from Rhacocarpus and Bartramiaceae species and to BGiesicke (Berlin) for technical assistance

References

BECKERT S H MUHLE D PRUCHNER amp V KNOOP (2001) The mitochondrial nad2 geneas a novel marker locus for phylogenetic analysis of early land plants a comparative analysis inmosses - Mol Phylogenet Evol 18 117-126

BELL NE amp AE NEWTON (2004) Systematic studies of non-hypnanaean pleurocarps establishinga phylogenetic framework for investigating the origins of pleurocarpy - In GOFFINET BV HOLLOWELL amp R MAGILL (eds) Molecular systematics of bryophytes Monogr Syst BotMissouri Bot Gard 98 290-319

BELL NE amp AE NEWTON (2007) Pleurocarpy in the Rhizogoniaceous grade - In NEWTONAE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolution SystematicsAssociation Special Volume Series 71 41-64

BELL NE D QUANDT TJ OBRIEN amp AE NEWTON (2007) Taxonomy and phylogeny inthe earliest diverging pleurocarps square holes and bifurcating pegs - Bryologist 110 533-560

BORSCH T KW HILU D QUANDT V WILDE C NEINHUIS amp W BARTHLOTT(2003) Non-coding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms- J Evol Biol 16 558-576

18

BUCK WR (2007) The history of pleurocarp classification two steps forward one step back - InNEWTON AE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 1-18

BUCK WR amp B GOFFINET (2000) Morphology and classification of mosses - In SHAWAJ amp B GOFFINET (eds) Bryophyte Biology pp 71-123 Cambridge University PressCambridge

CHIANG TY BA SCHAAL amp CI PENG (1998) Universal primers for amplification andsequencing a noncoding spacer between atpB and rbcL genes of chloroplast DNA - Bot Bull AcadSin 39 245-250

COX CJ B GOFFINET AE NEWTON AJ SHAW amp TAJ HEDDERSON (2000)Phylogenetic relationships among the diplolepideous-alternate mosses (Bryidae) inferred from nuclearand chloroplast DNA sequences - Bryologist 103 224-241

COX CJ B GOFFINET AJ SHAW amp SB BOLES (2004) Phylogenetic relationships amongthe mosses based on heterogeneous Bayesian analysis of multiple genes from multiple genomiccompartments - Syst Bot 29 234-250

CRANDALL-STOTLER B (1986) Morphogenesis developmental anatomy and bryophytephylogenetics contra-indications of monophyly - J Bryol 14 1-23

CROSBY MR RE MAGILL B ALLEN amp S HE (1999) A checklist of the mosses - MissouriBotanical Garden St Louis Missouri

DOWELD A (2001) Prosyllabus Tracheophytorum - GEOS Moscow i-lxxx + 110 pp

DOYLE JJ amp JL DOYLE (1990) Isolation of plant DNA from fresh tissue - Focus 12 13-15

DUFF RJ JC VILLAREAL DC CARGILL amp KS RENZAGLIA (2007) Progress andchallenges towards developing a phylogeny and classification of the hornworts - Bryologist 110214-243

FLEISCHER M (1920) Natuumlrliches System der Laubmoose - Hedwigia 61 390-400

FORREST LL EC DAVIS DG LONG BJ CRANDALL-STOTLER A CLARK ampML HOLLINGSWORTH (2006) Unraveling the evolutionary history of the liverworts (Marchantio-phyta) multiple taxa genomes and analyses - Bryologist 109 303-334

FRAHM J-P amp W FREY (1987) Moosflora 2 Aufl - UTB 1250 Stuttgart

FREY W (1977) Neue Vorstellungen uumlber die Verwandtschaftsgruppen und die Stammesgeschichteder Laubmoose - In FREY W H HURKA amp F OBERWINKLER (Hrsg) Beitraumlge zur Biologieder Pflanzen pp 117-139 Stuttgart

FREY W amp M STECH (2005) A morpho-molecular classification of the liverworts (Hepa-ticophytina Bryophyta) - Nova Hedwigia 81 55-78

FREY W M STECH amp K MEIszligNER (1999) Chloroplast DNA-relationship in palaeoaustralLopidium concinnum (Hypopterygiaceae Musci) An example of steno-evolution in mosses Studiesin austral temperate rain forest bryophytes 2 - Plant Syst Evol 218 67-75

GOFFINET B amp WR BUCK (2004) Systematics of Bryophyta (mosses) from molecules to arevised classification - In GOFFINET B V HOLLOWELL amp R MAGILL (eds) Molecularsystematics of bryophytes Monogr Syst Bot Missouri Bot Gard 98 205-239

GOFFINET B CJ COX AJ SHAW amp TAJ HEDDERSON (2001) The Bryophyta (mosses)Systematic and evolutionary inferences from an rps4 gene (cpDNA) phylogeny - Ann Bot 87191-208

GOFFINET B NJ WICKETT O WERNER RM ROS AJ SHAW amp CJ COX (2007)Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae(Bryophyta) - Ann Bot 99 747-753

19

GROTH-MALONEK M D PRUCHNER F GREWE amp V KNOOP (2005) Ancestors oftrans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosseswith vascular plants - Mol Biol Evol 22 117-125

HATTORI S amp H INOUE (1958) Preliminary report on Takakia lepidozioides - J Hattori BotLab 19 133-137

HE-NYGREacuteN X A JUSLEacuteN I AHONEN D GLENNY amp S PIIPPO (2006) Illuminating theevolutionary history of liverworts (Marchantiophyta) - towards a natural classification - Cladistics22 1-31

HEDDERSON TAJ DJ MURRAY CJ COX amp TL NOWELL (2004) Phylogeneticrelationships of haplolepideous mosses (Dicranidae) inferred from rps4 gene sequences - Syst Bot29 29-41

LA FARGE C BD MISHER JA WHEELER DP WALL K JOHANNES S SCHAFFERamp AJ SHAW (2000) Phylogenetic relationships within the haplolepideous mosses - Bryologist103 257-276

LA FARGE C AJ SHAW amp DH VITT (2002) The circumscription of the Dicranaceae(Bryopsida) based on the chloroplast regions trnL-trnF and rps4 - Syst Bot 27 435-452

MAGOMBO ZLK (2003) The phylogeny of basal peristomate mosses evidence from cpDNAand implications for peristome evolution - Syst Bot 28 24-38

MCNEILL J FR BARRIE HM BURDET V DEMOULIN DL HAWKSWORTHK MARHOLD DH NICOLSON J PRADO PC SILVA JE SKOG JH WIERSEMA ampNJ TURLAND (2006) International Code of Botanical Nomenclature (Vienna Code) - RegnumVegetabile 146 1-568

MUumlLLER K (2004) PRAP - computation of Bremer support for large data sets - Mol PhylogenetEvol 31 780-782

MUumlLLER K (2005) SeqState - primer design and sequence statistics for phylogenetic DNA datasets - Appl Bioinformatics 4 65-69

MUumlLLER K D QUANDT J MUumlLLER amp C NEINHUIS (2005) PhyDE v0992 PhylogeneticData Editor - httpwwwphydede

MURRAY BM (1988) Systematics of the Andreaeopsida (Bryophyta) two orders with links toTakakia - Nova Hedwigia Beih 90 289-336

NEWTON AE amp RS TANGNEY (eds) (2007) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 CRC Press Boca Raton 434 pp

NEWTON AE CJ COX JG DUCKETT JA WHEELER B GOFFINET TAJ HEDDER-SON amp BD MISHLER (2000) Evolution of the major moss lineages Phylogenetic analyses basedon multiple gene sequences and morphology - Bryologist 103 187-211

NEWTON AE N WIKSTROumlM NE BELL LL FORREST amp MS IGNATOV (2007)Dating the diversification of the pleurocarpous mosses - In NEWTON AE amp RS TANGNEY(eds) Pleurocarpous mosses systematics and evolution Systematics Association Special VolumeSeries 71 337-366

NIXON KC (1999) The parsimony ratchet a new method for rapid parsimony analysis - Cladistics15 407-411

OBRIEN TJ (2007) The phylogenetic distribution of pleurocarpous mosses evidence fromcpDNA sequences - In NEWTON AE amp RS TANGNEY (eds) Pleurocarpous mossessystematics and evolution Systematics Association Special Volume Series 71 19-41

OCHYRA R (2002) Nomenclatural changes in subfamilies of the Dicranaceae - CryptogamieBryol 23 345-349

20

OCHYRA R J ŻARNOWIEC amp H BEDNAREK-OCHYRA (2003) Census catalogue ofPolish mosses - Biodiv Poland 3 1-372

PEDERSEN N amp AE NEWTON (2007) Phylogenetic and morphological studies within thePtychomniales with emphasis on the evolution of dwarf males - In NEWTON AE amp RSTANGNEY (eds) Pleurocarpous mosses systematics and evolution Systematics AssociationSpecial Volume Series 71 367-392

QUANDT D amp M STECH (2005) Molecular evolution and secondary structure of the chloroplasttrnL intron in bryophytes - Mol Phylogenet Evol 36 429-443

QUANDT D K MUumlLLER amp S HUTTUNEN (2003) Characterisation of the chloroplast DNApsbT-H region and the influence of dyad symmetrical elements on phylogenetic reconstructions -Plant Biol 5 400-410

QUANDT D K MUumlLLER M STECH W FREY KW HILU amp T BORSCH (2004) Molecularevolution of the chloroplast trnL-F-region in land plants - In GOFFINET B V HOLLOWELL ampR MAGILL (eds) Molecular systematics of bryophytes Monogr Syst Bot Missouri Bot Gard98 13-37

QUANDT D NE BELL amp M STECH (2007) Unravelling the knot the Pulchrinodaceae famnov (Bryales) - In KUumlRSCHNER H T PFEIFFER amp M STECH (eds) A Festschrift to Wolf-gang Frey - a scientists life between deserts and rain forests Nova Hedwigia Beih 131 21-39

QIU Y-L Y CHO JC COX amp JD PALMER (1998) The gain of three mitochondrial intronsidentifies liverworts as the earliest land plants - Nature 394 671-674

QIU Y-L L LI B WANG Z CHEN V KNOOP M GROTH-MALONEK O DOM-BROVSKA J LEE L KENT J REST GF ESTABROOK TA HENDRY DW TAYLORCM TESTA M AMBROS B CRANDALL-STOTLER J DUFF M STECH W FREYD QUANDT amp CC DAVIS (2006) The deepest divergences in land plants inferred fromphylogenomic evidence - Proc Natl Acad Sci USA 103 15511-15516

RENZAGLIA KS S SCHUETTE RJ DUFF R LIGRONE AJ SHAW BD MISHLER ampJG DUCKETT (2007) Bryophyte phylogeny Advancing the molecular and morphological frontiers- Bryologist 110 179-213

SAMIGULLIN TH SP YACENTYUK GV DEGTYARYEVA KM VALIEJO-ROMANVK BOBROVA I CAPESIUS WF MARTIN AV TROITSKY VR FILIN amp ASANTONOV (2002) Paraphyly of bryophytes and close relationships of hornworts and vascularplants inferred from analysis of chloroplast rDNA ITS (cpITS) sequences - Arctoa 11 31-43

SANG T DJ CRAWFORD amp TF STUESSY (1997) Chloroplast DNA phylogeny reticulateevolution and biogeography of Paeonia (Paeoniaceae) - Amer J Bot 84 1120-1136

SHAW AJ amp KS RENZAGLIA (2004) Phylogeny and diversification of bryophytes - AmerJ Bot 91 1557-1581

SHAW AJ CJ COX amp B GOFFINET (2005) Global patterns of moss diversity taxonomic andmolecular inferences - Taxon 54 337-352

STECH M (1999a) A reclassification of Dicranaceae (Bryopsida) based on non-coding cpDNAsequence data - J Hattori Bot Lab 86 137-159

STECH M (1999b) A molecular systematic contribution to the position of Amphidium Schimp(Rhabdoweisiaceae Bryopsida) - Nova Hedwigia 68 291-300

STECH M (2004) Supraspecific circumscription and classification of Campylopus Brid(Dicranaceae Bryopsida) based on molecular data - Syst Bot 29 817-824

STECH M amp D QUANDT (2006) Molecular evolution of the chloroplast atpB-rbcL spacer inbryophytes - In SHARMA AK amp A SHARMA (eds) Plant Genome Biodiversity and EvolutionVol 2 Part B pp 409-431 Science Publishers Enfield New Hampshire

21

STECH M D QUANDT amp W FREY (2003) Molecular circumscription of the hornworts(Antho-cerotophyta) based on the chloroplast DNA trnL-trnF region - J Plant Res 116 389-398

STOTLER RE amp B CRANDALL-STOTLER (2005) A revised classification of theAnthocerotophyta and a checklist of the hornworts of North America north of Mexico - Bryologist108 16-26

SWOFFORD DL (2002) PAUP Phylogenetic analysis using parsimony (and other methods)version 40b10 - Sunderland MA

TABERLET P L GIELLY G PAUTOU amp J BOUVET (1991) Universal primers for amplificationof three non-coding regions of chloroplast DNA - Plant Mol Biol 17 1105-1109

TSUBOTA H Y AGENO B ESTEacuteBANEZ T YAMAGUCHI amp H DEGUCHI (2003)Molecular phylogeny of the Grimmiales (Musci) based on chloroplast rbcL sequences - Hikobia 1455-70

TSUBOTA H E DE LUNA D GONZAacuteLEZ MS IGNATOV amp H DEGUCHI (2004) Molecularphylogenetics and ordinal relationships based on analyses of a large-scale data set of 600 rbcLsequences of mosses - Hikobia 14 149-170

VITT DH (1984) Classification of the Bryopsida - In SCHUSTER RM (ed) New Manual ofBryology 2 696-759 Hattori Botanical Laboratory Nichinan Japan

VITT DH B GOFFINET amp T HEDDERSON (1998) 8 The ordinal classification of the mossesquestions and answers for the 1990s - In BATES JW NW ASHTON amp JG DUCKETT (eds)Bryology for the twenty-first century British Bryol Soc pp 113-123

Received 3 September 2007 accepted in revised form 30 October 2007

Page 16: botanica parcial 3

16

Order Grimmiales MFleischGrimmiaceae Arn Ptychomitriaceae Schimp Seligeriaceae Schimp

Order Archidiales LimprArchidiaceae Schimp

Order Mitteniales ShawMitteniaceae Broth

Order Dicranales HPhilib ex MFleischAmphidiaceae Stech Aongstroemiaceae De Not BruchiaceaeSchimp Calymperaceae Kindb Dicranaceae Schimp Dicranel-laceae Stech Ditrichaceae Limpr Erpodiaceae Broth EustichiaceaeBroth Fissidentaceae Schimp Leucobryaceae Schimp Onco-phoraceae Stech Rhachitheciaceae HRob Schistostegaceae SchimpViridivelleraceae IGStone Wardiaceae Welch

Order Pottiales MFleischEphemeraceae Schimp Hypodontiaceae Stech PleurophascaceaeBroth Pottiaceae Schimp Serpotortellaceae WDReese amp RHZander

Subclass Bryidae EnglOrder Hedwigiales Ochyra

Hedwigiaceae Schimp Rhacocarpaceae KindbOrder Helicophyllales Stech amp WFrey

Helicophyllaceae BrothOrder Bartramiales DQuandt NEBell amp Stech

Bartramiaceae SchwaumlgrOrder Splachnales Ochyra

Meesiaceae Schimp Splachnaceae Grev amp ArnOrder Bryales Limpr

Bryaceae Schwaumlgr Leptostomataceae Schwaumlgr Mniaceae SchwaumlgrPhyllodrepaniaceae Crosby Pseudoditrichaceae Steere amp ZIwatsPulchrinodaceae DQuandt NEBell amp Stech

Order Orthotrichales DixonOrthotrichaceae Arn

Order Orthodontiales NEBell AENewton amp DQuandtOrthodontiaceae Goffinet

Order Aulacomniales NEBell AENewton amp DQuandtAulacomniaceae Schimp

Order Rhizogoniales Goffinet amp WRBuckRhizogoniaceae Broth

Order Hypnodendrales NEBell AENewton amp DQuandtBraithwaiteaceae NEBell AENewton amp DQuandt Hypnodendra-ceae Broth Pterobryellaceae WRBuck amp Vitt Racopilaceae Kindb

Order Ptychomniales WRBuck CJCox AJShaw amp GoffinetPtychomniaceae MFleisch

Order Hookeriales MFleischDaltoniaceae Schimp Hookeriaceae Schimp HypopterygiaceaeMitt Leucomiaceae Broth Pilotrichaceae Kindb SaulomataceaeWRBuck CJCox AJShaw amp Goffinet Schimperobryaceae WR

17

Buck CJCox AJShaw amp GoffinetOrder Hypnales WRBuck amp Vitt

Amblystegiaceae GRoth Anomodontaceae Kindb BrachytheciaceaeSchimp Calliergonaceae Vanderpoorten Hedenaumls CJCox amp AJShaw Catagoniaceae WRBuck amp Ireland Climaciaceae KindbCryphaeaceae Schimp Echinodiaceae Broth Entodontaceae KindbFabroniaceae Schimp Fontinalaceae Schimp Helodiaceae OchyraHeterocladiaceae Ignatov amp Ignatova Hylocomiaceae MFleischHypnaceae Schimp Lembophyllaceae Broth LeptodontaceaeSchimp Lepyrodontaceae Broth Leskeaceae Schimp Leucodon-taceae Schimp Meteoriaceae Kindb Microtheciellaceae HAMillamp AJHarr Myriniaceae Schimp Myuriaceae MFleisch NeckeraceaeSchimp Orthorrhynchiaceae SHLin Phyllogoniaceae KindbPlagiotheciaceae MFleisch Pleuroziopsidaceae Ireland Prionodon-taceae Broth Pseudoleskeaceae Schimp PseudoleskeellaceaeIgnatov amp Ignatova Pterigynandraceae Schimp PterobryaceaeKindb Pylaisiaceae Schimp Pylaisiadelphaceae Goffinet amp WRBuck Regmatodontaceae Broth Rhytidiaceae Broth RigodiaceaeHACrum Rutenbergiaceae MFleisch Scorpidiaceae Ignatov ampIgnatova Sematophyllaceae Broth Sorapillaceae MFleisch Ste-reophyllaceae WRBuck amp Ireland Symphyodontaceae MFleischTheliaceae MFleisch Thuidiaceae Schimp TrachylomataceaeWRBuck amp Vitt

Acknowledgements

Sincere thanks are due to JLReveal (Ithaca) as well as WFPrudhomme van Reine and JFVeldkamp(Leiden) for comments and discussions about suprafamilial taxonomy to DQuandt (Dresden) for providingDNA from Rhacocarpus and Bartramiaceae species and to BGiesicke (Berlin) for technical assistance

References

BECKERT S H MUHLE D PRUCHNER amp V KNOOP (2001) The mitochondrial nad2 geneas a novel marker locus for phylogenetic analysis of early land plants a comparative analysis inmosses - Mol Phylogenet Evol 18 117-126

BELL NE amp AE NEWTON (2004) Systematic studies of non-hypnanaean pleurocarps establishinga phylogenetic framework for investigating the origins of pleurocarpy - In GOFFINET BV HOLLOWELL amp R MAGILL (eds) Molecular systematics of bryophytes Monogr Syst BotMissouri Bot Gard 98 290-319

BELL NE amp AE NEWTON (2007) Pleurocarpy in the Rhizogoniaceous grade - In NEWTONAE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolution SystematicsAssociation Special Volume Series 71 41-64

BELL NE D QUANDT TJ OBRIEN amp AE NEWTON (2007) Taxonomy and phylogeny inthe earliest diverging pleurocarps square holes and bifurcating pegs - Bryologist 110 533-560

BORSCH T KW HILU D QUANDT V WILDE C NEINHUIS amp W BARTHLOTT(2003) Non-coding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms- J Evol Biol 16 558-576

18

BUCK WR (2007) The history of pleurocarp classification two steps forward one step back - InNEWTON AE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 1-18

BUCK WR amp B GOFFINET (2000) Morphology and classification of mosses - In SHAWAJ amp B GOFFINET (eds) Bryophyte Biology pp 71-123 Cambridge University PressCambridge

CHIANG TY BA SCHAAL amp CI PENG (1998) Universal primers for amplification andsequencing a noncoding spacer between atpB and rbcL genes of chloroplast DNA - Bot Bull AcadSin 39 245-250

COX CJ B GOFFINET AE NEWTON AJ SHAW amp TAJ HEDDERSON (2000)Phylogenetic relationships among the diplolepideous-alternate mosses (Bryidae) inferred from nuclearand chloroplast DNA sequences - Bryologist 103 224-241

COX CJ B GOFFINET AJ SHAW amp SB BOLES (2004) Phylogenetic relationships amongthe mosses based on heterogeneous Bayesian analysis of multiple genes from multiple genomiccompartments - Syst Bot 29 234-250

CRANDALL-STOTLER B (1986) Morphogenesis developmental anatomy and bryophytephylogenetics contra-indications of monophyly - J Bryol 14 1-23

CROSBY MR RE MAGILL B ALLEN amp S HE (1999) A checklist of the mosses - MissouriBotanical Garden St Louis Missouri

DOWELD A (2001) Prosyllabus Tracheophytorum - GEOS Moscow i-lxxx + 110 pp

DOYLE JJ amp JL DOYLE (1990) Isolation of plant DNA from fresh tissue - Focus 12 13-15

DUFF RJ JC VILLAREAL DC CARGILL amp KS RENZAGLIA (2007) Progress andchallenges towards developing a phylogeny and classification of the hornworts - Bryologist 110214-243

FLEISCHER M (1920) Natuumlrliches System der Laubmoose - Hedwigia 61 390-400

FORREST LL EC DAVIS DG LONG BJ CRANDALL-STOTLER A CLARK ampML HOLLINGSWORTH (2006) Unraveling the evolutionary history of the liverworts (Marchantio-phyta) multiple taxa genomes and analyses - Bryologist 109 303-334

FRAHM J-P amp W FREY (1987) Moosflora 2 Aufl - UTB 1250 Stuttgart

FREY W (1977) Neue Vorstellungen uumlber die Verwandtschaftsgruppen und die Stammesgeschichteder Laubmoose - In FREY W H HURKA amp F OBERWINKLER (Hrsg) Beitraumlge zur Biologieder Pflanzen pp 117-139 Stuttgart

FREY W amp M STECH (2005) A morpho-molecular classification of the liverworts (Hepa-ticophytina Bryophyta) - Nova Hedwigia 81 55-78

FREY W M STECH amp K MEIszligNER (1999) Chloroplast DNA-relationship in palaeoaustralLopidium concinnum (Hypopterygiaceae Musci) An example of steno-evolution in mosses Studiesin austral temperate rain forest bryophytes 2 - Plant Syst Evol 218 67-75

GOFFINET B amp WR BUCK (2004) Systematics of Bryophyta (mosses) from molecules to arevised classification - In GOFFINET B V HOLLOWELL amp R MAGILL (eds) Molecularsystematics of bryophytes Monogr Syst Bot Missouri Bot Gard 98 205-239

GOFFINET B CJ COX AJ SHAW amp TAJ HEDDERSON (2001) The Bryophyta (mosses)Systematic and evolutionary inferences from an rps4 gene (cpDNA) phylogeny - Ann Bot 87191-208

GOFFINET B NJ WICKETT O WERNER RM ROS AJ SHAW amp CJ COX (2007)Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae(Bryophyta) - Ann Bot 99 747-753

19

GROTH-MALONEK M D PRUCHNER F GREWE amp V KNOOP (2005) Ancestors oftrans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosseswith vascular plants - Mol Biol Evol 22 117-125

HATTORI S amp H INOUE (1958) Preliminary report on Takakia lepidozioides - J Hattori BotLab 19 133-137

HE-NYGREacuteN X A JUSLEacuteN I AHONEN D GLENNY amp S PIIPPO (2006) Illuminating theevolutionary history of liverworts (Marchantiophyta) - towards a natural classification - Cladistics22 1-31

HEDDERSON TAJ DJ MURRAY CJ COX amp TL NOWELL (2004) Phylogeneticrelationships of haplolepideous mosses (Dicranidae) inferred from rps4 gene sequences - Syst Bot29 29-41

LA FARGE C BD MISHER JA WHEELER DP WALL K JOHANNES S SCHAFFERamp AJ SHAW (2000) Phylogenetic relationships within the haplolepideous mosses - Bryologist103 257-276

LA FARGE C AJ SHAW amp DH VITT (2002) The circumscription of the Dicranaceae(Bryopsida) based on the chloroplast regions trnL-trnF and rps4 - Syst Bot 27 435-452

MAGOMBO ZLK (2003) The phylogeny of basal peristomate mosses evidence from cpDNAand implications for peristome evolution - Syst Bot 28 24-38

MCNEILL J FR BARRIE HM BURDET V DEMOULIN DL HAWKSWORTHK MARHOLD DH NICOLSON J PRADO PC SILVA JE SKOG JH WIERSEMA ampNJ TURLAND (2006) International Code of Botanical Nomenclature (Vienna Code) - RegnumVegetabile 146 1-568

MUumlLLER K (2004) PRAP - computation of Bremer support for large data sets - Mol PhylogenetEvol 31 780-782

MUumlLLER K (2005) SeqState - primer design and sequence statistics for phylogenetic DNA datasets - Appl Bioinformatics 4 65-69

MUumlLLER K D QUANDT J MUumlLLER amp C NEINHUIS (2005) PhyDE v0992 PhylogeneticData Editor - httpwwwphydede

MURRAY BM (1988) Systematics of the Andreaeopsida (Bryophyta) two orders with links toTakakia - Nova Hedwigia Beih 90 289-336

NEWTON AE amp RS TANGNEY (eds) (2007) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 CRC Press Boca Raton 434 pp

NEWTON AE CJ COX JG DUCKETT JA WHEELER B GOFFINET TAJ HEDDER-SON amp BD MISHLER (2000) Evolution of the major moss lineages Phylogenetic analyses basedon multiple gene sequences and morphology - Bryologist 103 187-211

NEWTON AE N WIKSTROumlM NE BELL LL FORREST amp MS IGNATOV (2007)Dating the diversification of the pleurocarpous mosses - In NEWTON AE amp RS TANGNEY(eds) Pleurocarpous mosses systematics and evolution Systematics Association Special VolumeSeries 71 337-366

NIXON KC (1999) The parsimony ratchet a new method for rapid parsimony analysis - Cladistics15 407-411

OBRIEN TJ (2007) The phylogenetic distribution of pleurocarpous mosses evidence fromcpDNA sequences - In NEWTON AE amp RS TANGNEY (eds) Pleurocarpous mossessystematics and evolution Systematics Association Special Volume Series 71 19-41

OCHYRA R (2002) Nomenclatural changes in subfamilies of the Dicranaceae - CryptogamieBryol 23 345-349

20

OCHYRA R J ŻARNOWIEC amp H BEDNAREK-OCHYRA (2003) Census catalogue ofPolish mosses - Biodiv Poland 3 1-372

PEDERSEN N amp AE NEWTON (2007) Phylogenetic and morphological studies within thePtychomniales with emphasis on the evolution of dwarf males - In NEWTON AE amp RSTANGNEY (eds) Pleurocarpous mosses systematics and evolution Systematics AssociationSpecial Volume Series 71 367-392

QUANDT D amp M STECH (2005) Molecular evolution and secondary structure of the chloroplasttrnL intron in bryophytes - Mol Phylogenet Evol 36 429-443

QUANDT D K MUumlLLER amp S HUTTUNEN (2003) Characterisation of the chloroplast DNApsbT-H region and the influence of dyad symmetrical elements on phylogenetic reconstructions -Plant Biol 5 400-410

QUANDT D K MUumlLLER M STECH W FREY KW HILU amp T BORSCH (2004) Molecularevolution of the chloroplast trnL-F-region in land plants - In GOFFINET B V HOLLOWELL ampR MAGILL (eds) Molecular systematics of bryophytes Monogr Syst Bot Missouri Bot Gard98 13-37

QUANDT D NE BELL amp M STECH (2007) Unravelling the knot the Pulchrinodaceae famnov (Bryales) - In KUumlRSCHNER H T PFEIFFER amp M STECH (eds) A Festschrift to Wolf-gang Frey - a scientists life between deserts and rain forests Nova Hedwigia Beih 131 21-39

QIU Y-L Y CHO JC COX amp JD PALMER (1998) The gain of three mitochondrial intronsidentifies liverworts as the earliest land plants - Nature 394 671-674

QIU Y-L L LI B WANG Z CHEN V KNOOP M GROTH-MALONEK O DOM-BROVSKA J LEE L KENT J REST GF ESTABROOK TA HENDRY DW TAYLORCM TESTA M AMBROS B CRANDALL-STOTLER J DUFF M STECH W FREYD QUANDT amp CC DAVIS (2006) The deepest divergences in land plants inferred fromphylogenomic evidence - Proc Natl Acad Sci USA 103 15511-15516

RENZAGLIA KS S SCHUETTE RJ DUFF R LIGRONE AJ SHAW BD MISHLER ampJG DUCKETT (2007) Bryophyte phylogeny Advancing the molecular and morphological frontiers- Bryologist 110 179-213

SAMIGULLIN TH SP YACENTYUK GV DEGTYARYEVA KM VALIEJO-ROMANVK BOBROVA I CAPESIUS WF MARTIN AV TROITSKY VR FILIN amp ASANTONOV (2002) Paraphyly of bryophytes and close relationships of hornworts and vascularplants inferred from analysis of chloroplast rDNA ITS (cpITS) sequences - Arctoa 11 31-43

SANG T DJ CRAWFORD amp TF STUESSY (1997) Chloroplast DNA phylogeny reticulateevolution and biogeography of Paeonia (Paeoniaceae) - Amer J Bot 84 1120-1136

SHAW AJ amp KS RENZAGLIA (2004) Phylogeny and diversification of bryophytes - AmerJ Bot 91 1557-1581

SHAW AJ CJ COX amp B GOFFINET (2005) Global patterns of moss diversity taxonomic andmolecular inferences - Taxon 54 337-352

STECH M (1999a) A reclassification of Dicranaceae (Bryopsida) based on non-coding cpDNAsequence data - J Hattori Bot Lab 86 137-159

STECH M (1999b) A molecular systematic contribution to the position of Amphidium Schimp(Rhabdoweisiaceae Bryopsida) - Nova Hedwigia 68 291-300

STECH M (2004) Supraspecific circumscription and classification of Campylopus Brid(Dicranaceae Bryopsida) based on molecular data - Syst Bot 29 817-824

STECH M amp D QUANDT (2006) Molecular evolution of the chloroplast atpB-rbcL spacer inbryophytes - In SHARMA AK amp A SHARMA (eds) Plant Genome Biodiversity and EvolutionVol 2 Part B pp 409-431 Science Publishers Enfield New Hampshire

21

STECH M D QUANDT amp W FREY (2003) Molecular circumscription of the hornworts(Antho-cerotophyta) based on the chloroplast DNA trnL-trnF region - J Plant Res 116 389-398

STOTLER RE amp B CRANDALL-STOTLER (2005) A revised classification of theAnthocerotophyta and a checklist of the hornworts of North America north of Mexico - Bryologist108 16-26

SWOFFORD DL (2002) PAUP Phylogenetic analysis using parsimony (and other methods)version 40b10 - Sunderland MA

TABERLET P L GIELLY G PAUTOU amp J BOUVET (1991) Universal primers for amplificationof three non-coding regions of chloroplast DNA - Plant Mol Biol 17 1105-1109

TSUBOTA H Y AGENO B ESTEacuteBANEZ T YAMAGUCHI amp H DEGUCHI (2003)Molecular phylogeny of the Grimmiales (Musci) based on chloroplast rbcL sequences - Hikobia 1455-70

TSUBOTA H E DE LUNA D GONZAacuteLEZ MS IGNATOV amp H DEGUCHI (2004) Molecularphylogenetics and ordinal relationships based on analyses of a large-scale data set of 600 rbcLsequences of mosses - Hikobia 14 149-170

VITT DH (1984) Classification of the Bryopsida - In SCHUSTER RM (ed) New Manual ofBryology 2 696-759 Hattori Botanical Laboratory Nichinan Japan

VITT DH B GOFFINET amp T HEDDERSON (1998) 8 The ordinal classification of the mossesquestions and answers for the 1990s - In BATES JW NW ASHTON amp JG DUCKETT (eds)Bryology for the twenty-first century British Bryol Soc pp 113-123

Received 3 September 2007 accepted in revised form 30 October 2007

Page 17: botanica parcial 3

17

Buck CJCox AJShaw amp GoffinetOrder Hypnales WRBuck amp Vitt

Amblystegiaceae GRoth Anomodontaceae Kindb BrachytheciaceaeSchimp Calliergonaceae Vanderpoorten Hedenaumls CJCox amp AJShaw Catagoniaceae WRBuck amp Ireland Climaciaceae KindbCryphaeaceae Schimp Echinodiaceae Broth Entodontaceae KindbFabroniaceae Schimp Fontinalaceae Schimp Helodiaceae OchyraHeterocladiaceae Ignatov amp Ignatova Hylocomiaceae MFleischHypnaceae Schimp Lembophyllaceae Broth LeptodontaceaeSchimp Lepyrodontaceae Broth Leskeaceae Schimp Leucodon-taceae Schimp Meteoriaceae Kindb Microtheciellaceae HAMillamp AJHarr Myriniaceae Schimp Myuriaceae MFleisch NeckeraceaeSchimp Orthorrhynchiaceae SHLin Phyllogoniaceae KindbPlagiotheciaceae MFleisch Pleuroziopsidaceae Ireland Prionodon-taceae Broth Pseudoleskeaceae Schimp PseudoleskeellaceaeIgnatov amp Ignatova Pterigynandraceae Schimp PterobryaceaeKindb Pylaisiaceae Schimp Pylaisiadelphaceae Goffinet amp WRBuck Regmatodontaceae Broth Rhytidiaceae Broth RigodiaceaeHACrum Rutenbergiaceae MFleisch Scorpidiaceae Ignatov ampIgnatova Sematophyllaceae Broth Sorapillaceae MFleisch Ste-reophyllaceae WRBuck amp Ireland Symphyodontaceae MFleischTheliaceae MFleisch Thuidiaceae Schimp TrachylomataceaeWRBuck amp Vitt

Acknowledgements

Sincere thanks are due to JLReveal (Ithaca) as well as WFPrudhomme van Reine and JFVeldkamp(Leiden) for comments and discussions about suprafamilial taxonomy to DQuandt (Dresden) for providingDNA from Rhacocarpus and Bartramiaceae species and to BGiesicke (Berlin) for technical assistance

References

BECKERT S H MUHLE D PRUCHNER amp V KNOOP (2001) The mitochondrial nad2 geneas a novel marker locus for phylogenetic analysis of early land plants a comparative analysis inmosses - Mol Phylogenet Evol 18 117-126

BELL NE amp AE NEWTON (2004) Systematic studies of non-hypnanaean pleurocarps establishinga phylogenetic framework for investigating the origins of pleurocarpy - In GOFFINET BV HOLLOWELL amp R MAGILL (eds) Molecular systematics of bryophytes Monogr Syst BotMissouri Bot Gard 98 290-319

BELL NE amp AE NEWTON (2007) Pleurocarpy in the Rhizogoniaceous grade - In NEWTONAE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolution SystematicsAssociation Special Volume Series 71 41-64

BELL NE D QUANDT TJ OBRIEN amp AE NEWTON (2007) Taxonomy and phylogeny inthe earliest diverging pleurocarps square holes and bifurcating pegs - Bryologist 110 533-560

BORSCH T KW HILU D QUANDT V WILDE C NEINHUIS amp W BARTHLOTT(2003) Non-coding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms- J Evol Biol 16 558-576

18

BUCK WR (2007) The history of pleurocarp classification two steps forward one step back - InNEWTON AE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 1-18

BUCK WR amp B GOFFINET (2000) Morphology and classification of mosses - In SHAWAJ amp B GOFFINET (eds) Bryophyte Biology pp 71-123 Cambridge University PressCambridge

CHIANG TY BA SCHAAL amp CI PENG (1998) Universal primers for amplification andsequencing a noncoding spacer between atpB and rbcL genes of chloroplast DNA - Bot Bull AcadSin 39 245-250

COX CJ B GOFFINET AE NEWTON AJ SHAW amp TAJ HEDDERSON (2000)Phylogenetic relationships among the diplolepideous-alternate mosses (Bryidae) inferred from nuclearand chloroplast DNA sequences - Bryologist 103 224-241

COX CJ B GOFFINET AJ SHAW amp SB BOLES (2004) Phylogenetic relationships amongthe mosses based on heterogeneous Bayesian analysis of multiple genes from multiple genomiccompartments - Syst Bot 29 234-250

CRANDALL-STOTLER B (1986) Morphogenesis developmental anatomy and bryophytephylogenetics contra-indications of monophyly - J Bryol 14 1-23

CROSBY MR RE MAGILL B ALLEN amp S HE (1999) A checklist of the mosses - MissouriBotanical Garden St Louis Missouri

DOWELD A (2001) Prosyllabus Tracheophytorum - GEOS Moscow i-lxxx + 110 pp

DOYLE JJ amp JL DOYLE (1990) Isolation of plant DNA from fresh tissue - Focus 12 13-15

DUFF RJ JC VILLAREAL DC CARGILL amp KS RENZAGLIA (2007) Progress andchallenges towards developing a phylogeny and classification of the hornworts - Bryologist 110214-243

FLEISCHER M (1920) Natuumlrliches System der Laubmoose - Hedwigia 61 390-400

FORREST LL EC DAVIS DG LONG BJ CRANDALL-STOTLER A CLARK ampML HOLLINGSWORTH (2006) Unraveling the evolutionary history of the liverworts (Marchantio-phyta) multiple taxa genomes and analyses - Bryologist 109 303-334

FRAHM J-P amp W FREY (1987) Moosflora 2 Aufl - UTB 1250 Stuttgart

FREY W (1977) Neue Vorstellungen uumlber die Verwandtschaftsgruppen und die Stammesgeschichteder Laubmoose - In FREY W H HURKA amp F OBERWINKLER (Hrsg) Beitraumlge zur Biologieder Pflanzen pp 117-139 Stuttgart

FREY W amp M STECH (2005) A morpho-molecular classification of the liverworts (Hepa-ticophytina Bryophyta) - Nova Hedwigia 81 55-78

FREY W M STECH amp K MEIszligNER (1999) Chloroplast DNA-relationship in palaeoaustralLopidium concinnum (Hypopterygiaceae Musci) An example of steno-evolution in mosses Studiesin austral temperate rain forest bryophytes 2 - Plant Syst Evol 218 67-75

GOFFINET B amp WR BUCK (2004) Systematics of Bryophyta (mosses) from molecules to arevised classification - In GOFFINET B V HOLLOWELL amp R MAGILL (eds) Molecularsystematics of bryophytes Monogr Syst Bot Missouri Bot Gard 98 205-239

GOFFINET B CJ COX AJ SHAW amp TAJ HEDDERSON (2001) The Bryophyta (mosses)Systematic and evolutionary inferences from an rps4 gene (cpDNA) phylogeny - Ann Bot 87191-208

GOFFINET B NJ WICKETT O WERNER RM ROS AJ SHAW amp CJ COX (2007)Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae(Bryophyta) - Ann Bot 99 747-753

19

GROTH-MALONEK M D PRUCHNER F GREWE amp V KNOOP (2005) Ancestors oftrans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosseswith vascular plants - Mol Biol Evol 22 117-125

HATTORI S amp H INOUE (1958) Preliminary report on Takakia lepidozioides - J Hattori BotLab 19 133-137

HE-NYGREacuteN X A JUSLEacuteN I AHONEN D GLENNY amp S PIIPPO (2006) Illuminating theevolutionary history of liverworts (Marchantiophyta) - towards a natural classification - Cladistics22 1-31

HEDDERSON TAJ DJ MURRAY CJ COX amp TL NOWELL (2004) Phylogeneticrelationships of haplolepideous mosses (Dicranidae) inferred from rps4 gene sequences - Syst Bot29 29-41

LA FARGE C BD MISHER JA WHEELER DP WALL K JOHANNES S SCHAFFERamp AJ SHAW (2000) Phylogenetic relationships within the haplolepideous mosses - Bryologist103 257-276

LA FARGE C AJ SHAW amp DH VITT (2002) The circumscription of the Dicranaceae(Bryopsida) based on the chloroplast regions trnL-trnF and rps4 - Syst Bot 27 435-452

MAGOMBO ZLK (2003) The phylogeny of basal peristomate mosses evidence from cpDNAand implications for peristome evolution - Syst Bot 28 24-38

MCNEILL J FR BARRIE HM BURDET V DEMOULIN DL HAWKSWORTHK MARHOLD DH NICOLSON J PRADO PC SILVA JE SKOG JH WIERSEMA ampNJ TURLAND (2006) International Code of Botanical Nomenclature (Vienna Code) - RegnumVegetabile 146 1-568

MUumlLLER K (2004) PRAP - computation of Bremer support for large data sets - Mol PhylogenetEvol 31 780-782

MUumlLLER K (2005) SeqState - primer design and sequence statistics for phylogenetic DNA datasets - Appl Bioinformatics 4 65-69

MUumlLLER K D QUANDT J MUumlLLER amp C NEINHUIS (2005) PhyDE v0992 PhylogeneticData Editor - httpwwwphydede

MURRAY BM (1988) Systematics of the Andreaeopsida (Bryophyta) two orders with links toTakakia - Nova Hedwigia Beih 90 289-336

NEWTON AE amp RS TANGNEY (eds) (2007) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 CRC Press Boca Raton 434 pp

NEWTON AE CJ COX JG DUCKETT JA WHEELER B GOFFINET TAJ HEDDER-SON amp BD MISHLER (2000) Evolution of the major moss lineages Phylogenetic analyses basedon multiple gene sequences and morphology - Bryologist 103 187-211

NEWTON AE N WIKSTROumlM NE BELL LL FORREST amp MS IGNATOV (2007)Dating the diversification of the pleurocarpous mosses - In NEWTON AE amp RS TANGNEY(eds) Pleurocarpous mosses systematics and evolution Systematics Association Special VolumeSeries 71 337-366

NIXON KC (1999) The parsimony ratchet a new method for rapid parsimony analysis - Cladistics15 407-411

OBRIEN TJ (2007) The phylogenetic distribution of pleurocarpous mosses evidence fromcpDNA sequences - In NEWTON AE amp RS TANGNEY (eds) Pleurocarpous mossessystematics and evolution Systematics Association Special Volume Series 71 19-41

OCHYRA R (2002) Nomenclatural changes in subfamilies of the Dicranaceae - CryptogamieBryol 23 345-349

20

OCHYRA R J ŻARNOWIEC amp H BEDNAREK-OCHYRA (2003) Census catalogue ofPolish mosses - Biodiv Poland 3 1-372

PEDERSEN N amp AE NEWTON (2007) Phylogenetic and morphological studies within thePtychomniales with emphasis on the evolution of dwarf males - In NEWTON AE amp RSTANGNEY (eds) Pleurocarpous mosses systematics and evolution Systematics AssociationSpecial Volume Series 71 367-392

QUANDT D amp M STECH (2005) Molecular evolution and secondary structure of the chloroplasttrnL intron in bryophytes - Mol Phylogenet Evol 36 429-443

QUANDT D K MUumlLLER amp S HUTTUNEN (2003) Characterisation of the chloroplast DNApsbT-H region and the influence of dyad symmetrical elements on phylogenetic reconstructions -Plant Biol 5 400-410

QUANDT D K MUumlLLER M STECH W FREY KW HILU amp T BORSCH (2004) Molecularevolution of the chloroplast trnL-F-region in land plants - In GOFFINET B V HOLLOWELL ampR MAGILL (eds) Molecular systematics of bryophytes Monogr Syst Bot Missouri Bot Gard98 13-37

QUANDT D NE BELL amp M STECH (2007) Unravelling the knot the Pulchrinodaceae famnov (Bryales) - In KUumlRSCHNER H T PFEIFFER amp M STECH (eds) A Festschrift to Wolf-gang Frey - a scientists life between deserts and rain forests Nova Hedwigia Beih 131 21-39

QIU Y-L Y CHO JC COX amp JD PALMER (1998) The gain of three mitochondrial intronsidentifies liverworts as the earliest land plants - Nature 394 671-674

QIU Y-L L LI B WANG Z CHEN V KNOOP M GROTH-MALONEK O DOM-BROVSKA J LEE L KENT J REST GF ESTABROOK TA HENDRY DW TAYLORCM TESTA M AMBROS B CRANDALL-STOTLER J DUFF M STECH W FREYD QUANDT amp CC DAVIS (2006) The deepest divergences in land plants inferred fromphylogenomic evidence - Proc Natl Acad Sci USA 103 15511-15516

RENZAGLIA KS S SCHUETTE RJ DUFF R LIGRONE AJ SHAW BD MISHLER ampJG DUCKETT (2007) Bryophyte phylogeny Advancing the molecular and morphological frontiers- Bryologist 110 179-213

SAMIGULLIN TH SP YACENTYUK GV DEGTYARYEVA KM VALIEJO-ROMANVK BOBROVA I CAPESIUS WF MARTIN AV TROITSKY VR FILIN amp ASANTONOV (2002) Paraphyly of bryophytes and close relationships of hornworts and vascularplants inferred from analysis of chloroplast rDNA ITS (cpITS) sequences - Arctoa 11 31-43

SANG T DJ CRAWFORD amp TF STUESSY (1997) Chloroplast DNA phylogeny reticulateevolution and biogeography of Paeonia (Paeoniaceae) - Amer J Bot 84 1120-1136

SHAW AJ amp KS RENZAGLIA (2004) Phylogeny and diversification of bryophytes - AmerJ Bot 91 1557-1581

SHAW AJ CJ COX amp B GOFFINET (2005) Global patterns of moss diversity taxonomic andmolecular inferences - Taxon 54 337-352

STECH M (1999a) A reclassification of Dicranaceae (Bryopsida) based on non-coding cpDNAsequence data - J Hattori Bot Lab 86 137-159

STECH M (1999b) A molecular systematic contribution to the position of Amphidium Schimp(Rhabdoweisiaceae Bryopsida) - Nova Hedwigia 68 291-300

STECH M (2004) Supraspecific circumscription and classification of Campylopus Brid(Dicranaceae Bryopsida) based on molecular data - Syst Bot 29 817-824

STECH M amp D QUANDT (2006) Molecular evolution of the chloroplast atpB-rbcL spacer inbryophytes - In SHARMA AK amp A SHARMA (eds) Plant Genome Biodiversity and EvolutionVol 2 Part B pp 409-431 Science Publishers Enfield New Hampshire

21

STECH M D QUANDT amp W FREY (2003) Molecular circumscription of the hornworts(Antho-cerotophyta) based on the chloroplast DNA trnL-trnF region - J Plant Res 116 389-398

STOTLER RE amp B CRANDALL-STOTLER (2005) A revised classification of theAnthocerotophyta and a checklist of the hornworts of North America north of Mexico - Bryologist108 16-26

SWOFFORD DL (2002) PAUP Phylogenetic analysis using parsimony (and other methods)version 40b10 - Sunderland MA

TABERLET P L GIELLY G PAUTOU amp J BOUVET (1991) Universal primers for amplificationof three non-coding regions of chloroplast DNA - Plant Mol Biol 17 1105-1109

TSUBOTA H Y AGENO B ESTEacuteBANEZ T YAMAGUCHI amp H DEGUCHI (2003)Molecular phylogeny of the Grimmiales (Musci) based on chloroplast rbcL sequences - Hikobia 1455-70

TSUBOTA H E DE LUNA D GONZAacuteLEZ MS IGNATOV amp H DEGUCHI (2004) Molecularphylogenetics and ordinal relationships based on analyses of a large-scale data set of 600 rbcLsequences of mosses - Hikobia 14 149-170

VITT DH (1984) Classification of the Bryopsida - In SCHUSTER RM (ed) New Manual ofBryology 2 696-759 Hattori Botanical Laboratory Nichinan Japan

VITT DH B GOFFINET amp T HEDDERSON (1998) 8 The ordinal classification of the mossesquestions and answers for the 1990s - In BATES JW NW ASHTON amp JG DUCKETT (eds)Bryology for the twenty-first century British Bryol Soc pp 113-123

Received 3 September 2007 accepted in revised form 30 October 2007

Page 18: botanica parcial 3

18

BUCK WR (2007) The history of pleurocarp classification two steps forward one step back - InNEWTON AE amp RS TANGNEY (eds) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 1-18

BUCK WR amp B GOFFINET (2000) Morphology and classification of mosses - In SHAWAJ amp B GOFFINET (eds) Bryophyte Biology pp 71-123 Cambridge University PressCambridge

CHIANG TY BA SCHAAL amp CI PENG (1998) Universal primers for amplification andsequencing a noncoding spacer between atpB and rbcL genes of chloroplast DNA - Bot Bull AcadSin 39 245-250

COX CJ B GOFFINET AE NEWTON AJ SHAW amp TAJ HEDDERSON (2000)Phylogenetic relationships among the diplolepideous-alternate mosses (Bryidae) inferred from nuclearand chloroplast DNA sequences - Bryologist 103 224-241

COX CJ B GOFFINET AJ SHAW amp SB BOLES (2004) Phylogenetic relationships amongthe mosses based on heterogeneous Bayesian analysis of multiple genes from multiple genomiccompartments - Syst Bot 29 234-250

CRANDALL-STOTLER B (1986) Morphogenesis developmental anatomy and bryophytephylogenetics contra-indications of monophyly - J Bryol 14 1-23

CROSBY MR RE MAGILL B ALLEN amp S HE (1999) A checklist of the mosses - MissouriBotanical Garden St Louis Missouri

DOWELD A (2001) Prosyllabus Tracheophytorum - GEOS Moscow i-lxxx + 110 pp

DOYLE JJ amp JL DOYLE (1990) Isolation of plant DNA from fresh tissue - Focus 12 13-15

DUFF RJ JC VILLAREAL DC CARGILL amp KS RENZAGLIA (2007) Progress andchallenges towards developing a phylogeny and classification of the hornworts - Bryologist 110214-243

FLEISCHER M (1920) Natuumlrliches System der Laubmoose - Hedwigia 61 390-400

FORREST LL EC DAVIS DG LONG BJ CRANDALL-STOTLER A CLARK ampML HOLLINGSWORTH (2006) Unraveling the evolutionary history of the liverworts (Marchantio-phyta) multiple taxa genomes and analyses - Bryologist 109 303-334

FRAHM J-P amp W FREY (1987) Moosflora 2 Aufl - UTB 1250 Stuttgart

FREY W (1977) Neue Vorstellungen uumlber die Verwandtschaftsgruppen und die Stammesgeschichteder Laubmoose - In FREY W H HURKA amp F OBERWINKLER (Hrsg) Beitraumlge zur Biologieder Pflanzen pp 117-139 Stuttgart

FREY W amp M STECH (2005) A morpho-molecular classification of the liverworts (Hepa-ticophytina Bryophyta) - Nova Hedwigia 81 55-78

FREY W M STECH amp K MEIszligNER (1999) Chloroplast DNA-relationship in palaeoaustralLopidium concinnum (Hypopterygiaceae Musci) An example of steno-evolution in mosses Studiesin austral temperate rain forest bryophytes 2 - Plant Syst Evol 218 67-75

GOFFINET B amp WR BUCK (2004) Systematics of Bryophyta (mosses) from molecules to arevised classification - In GOFFINET B V HOLLOWELL amp R MAGILL (eds) Molecularsystematics of bryophytes Monogr Syst Bot Missouri Bot Gard 98 205-239

GOFFINET B CJ COX AJ SHAW amp TAJ HEDDERSON (2001) The Bryophyta (mosses)Systematic and evolutionary inferences from an rps4 gene (cpDNA) phylogeny - Ann Bot 87191-208

GOFFINET B NJ WICKETT O WERNER RM ROS AJ SHAW amp CJ COX (2007)Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae(Bryophyta) - Ann Bot 99 747-753

19

GROTH-MALONEK M D PRUCHNER F GREWE amp V KNOOP (2005) Ancestors oftrans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosseswith vascular plants - Mol Biol Evol 22 117-125

HATTORI S amp H INOUE (1958) Preliminary report on Takakia lepidozioides - J Hattori BotLab 19 133-137

HE-NYGREacuteN X A JUSLEacuteN I AHONEN D GLENNY amp S PIIPPO (2006) Illuminating theevolutionary history of liverworts (Marchantiophyta) - towards a natural classification - Cladistics22 1-31

HEDDERSON TAJ DJ MURRAY CJ COX amp TL NOWELL (2004) Phylogeneticrelationships of haplolepideous mosses (Dicranidae) inferred from rps4 gene sequences - Syst Bot29 29-41

LA FARGE C BD MISHER JA WHEELER DP WALL K JOHANNES S SCHAFFERamp AJ SHAW (2000) Phylogenetic relationships within the haplolepideous mosses - Bryologist103 257-276

LA FARGE C AJ SHAW amp DH VITT (2002) The circumscription of the Dicranaceae(Bryopsida) based on the chloroplast regions trnL-trnF and rps4 - Syst Bot 27 435-452

MAGOMBO ZLK (2003) The phylogeny of basal peristomate mosses evidence from cpDNAand implications for peristome evolution - Syst Bot 28 24-38

MCNEILL J FR BARRIE HM BURDET V DEMOULIN DL HAWKSWORTHK MARHOLD DH NICOLSON J PRADO PC SILVA JE SKOG JH WIERSEMA ampNJ TURLAND (2006) International Code of Botanical Nomenclature (Vienna Code) - RegnumVegetabile 146 1-568

MUumlLLER K (2004) PRAP - computation of Bremer support for large data sets - Mol PhylogenetEvol 31 780-782

MUumlLLER K (2005) SeqState - primer design and sequence statistics for phylogenetic DNA datasets - Appl Bioinformatics 4 65-69

MUumlLLER K D QUANDT J MUumlLLER amp C NEINHUIS (2005) PhyDE v0992 PhylogeneticData Editor - httpwwwphydede

MURRAY BM (1988) Systematics of the Andreaeopsida (Bryophyta) two orders with links toTakakia - Nova Hedwigia Beih 90 289-336

NEWTON AE amp RS TANGNEY (eds) (2007) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 CRC Press Boca Raton 434 pp

NEWTON AE CJ COX JG DUCKETT JA WHEELER B GOFFINET TAJ HEDDER-SON amp BD MISHLER (2000) Evolution of the major moss lineages Phylogenetic analyses basedon multiple gene sequences and morphology - Bryologist 103 187-211

NEWTON AE N WIKSTROumlM NE BELL LL FORREST amp MS IGNATOV (2007)Dating the diversification of the pleurocarpous mosses - In NEWTON AE amp RS TANGNEY(eds) Pleurocarpous mosses systematics and evolution Systematics Association Special VolumeSeries 71 337-366

NIXON KC (1999) The parsimony ratchet a new method for rapid parsimony analysis - Cladistics15 407-411

OBRIEN TJ (2007) The phylogenetic distribution of pleurocarpous mosses evidence fromcpDNA sequences - In NEWTON AE amp RS TANGNEY (eds) Pleurocarpous mossessystematics and evolution Systematics Association Special Volume Series 71 19-41

OCHYRA R (2002) Nomenclatural changes in subfamilies of the Dicranaceae - CryptogamieBryol 23 345-349

20

OCHYRA R J ŻARNOWIEC amp H BEDNAREK-OCHYRA (2003) Census catalogue ofPolish mosses - Biodiv Poland 3 1-372

PEDERSEN N amp AE NEWTON (2007) Phylogenetic and morphological studies within thePtychomniales with emphasis on the evolution of dwarf males - In NEWTON AE amp RSTANGNEY (eds) Pleurocarpous mosses systematics and evolution Systematics AssociationSpecial Volume Series 71 367-392

QUANDT D amp M STECH (2005) Molecular evolution and secondary structure of the chloroplasttrnL intron in bryophytes - Mol Phylogenet Evol 36 429-443

QUANDT D K MUumlLLER amp S HUTTUNEN (2003) Characterisation of the chloroplast DNApsbT-H region and the influence of dyad symmetrical elements on phylogenetic reconstructions -Plant Biol 5 400-410

QUANDT D K MUumlLLER M STECH W FREY KW HILU amp T BORSCH (2004) Molecularevolution of the chloroplast trnL-F-region in land plants - In GOFFINET B V HOLLOWELL ampR MAGILL (eds) Molecular systematics of bryophytes Monogr Syst Bot Missouri Bot Gard98 13-37

QUANDT D NE BELL amp M STECH (2007) Unravelling the knot the Pulchrinodaceae famnov (Bryales) - In KUumlRSCHNER H T PFEIFFER amp M STECH (eds) A Festschrift to Wolf-gang Frey - a scientists life between deserts and rain forests Nova Hedwigia Beih 131 21-39

QIU Y-L Y CHO JC COX amp JD PALMER (1998) The gain of three mitochondrial intronsidentifies liverworts as the earliest land plants - Nature 394 671-674

QIU Y-L L LI B WANG Z CHEN V KNOOP M GROTH-MALONEK O DOM-BROVSKA J LEE L KENT J REST GF ESTABROOK TA HENDRY DW TAYLORCM TESTA M AMBROS B CRANDALL-STOTLER J DUFF M STECH W FREYD QUANDT amp CC DAVIS (2006) The deepest divergences in land plants inferred fromphylogenomic evidence - Proc Natl Acad Sci USA 103 15511-15516

RENZAGLIA KS S SCHUETTE RJ DUFF R LIGRONE AJ SHAW BD MISHLER ampJG DUCKETT (2007) Bryophyte phylogeny Advancing the molecular and morphological frontiers- Bryologist 110 179-213

SAMIGULLIN TH SP YACENTYUK GV DEGTYARYEVA KM VALIEJO-ROMANVK BOBROVA I CAPESIUS WF MARTIN AV TROITSKY VR FILIN amp ASANTONOV (2002) Paraphyly of bryophytes and close relationships of hornworts and vascularplants inferred from analysis of chloroplast rDNA ITS (cpITS) sequences - Arctoa 11 31-43

SANG T DJ CRAWFORD amp TF STUESSY (1997) Chloroplast DNA phylogeny reticulateevolution and biogeography of Paeonia (Paeoniaceae) - Amer J Bot 84 1120-1136

SHAW AJ amp KS RENZAGLIA (2004) Phylogeny and diversification of bryophytes - AmerJ Bot 91 1557-1581

SHAW AJ CJ COX amp B GOFFINET (2005) Global patterns of moss diversity taxonomic andmolecular inferences - Taxon 54 337-352

STECH M (1999a) A reclassification of Dicranaceae (Bryopsida) based on non-coding cpDNAsequence data - J Hattori Bot Lab 86 137-159

STECH M (1999b) A molecular systematic contribution to the position of Amphidium Schimp(Rhabdoweisiaceae Bryopsida) - Nova Hedwigia 68 291-300

STECH M (2004) Supraspecific circumscription and classification of Campylopus Brid(Dicranaceae Bryopsida) based on molecular data - Syst Bot 29 817-824

STECH M amp D QUANDT (2006) Molecular evolution of the chloroplast atpB-rbcL spacer inbryophytes - In SHARMA AK amp A SHARMA (eds) Plant Genome Biodiversity and EvolutionVol 2 Part B pp 409-431 Science Publishers Enfield New Hampshire

21

STECH M D QUANDT amp W FREY (2003) Molecular circumscription of the hornworts(Antho-cerotophyta) based on the chloroplast DNA trnL-trnF region - J Plant Res 116 389-398

STOTLER RE amp B CRANDALL-STOTLER (2005) A revised classification of theAnthocerotophyta and a checklist of the hornworts of North America north of Mexico - Bryologist108 16-26

SWOFFORD DL (2002) PAUP Phylogenetic analysis using parsimony (and other methods)version 40b10 - Sunderland MA

TABERLET P L GIELLY G PAUTOU amp J BOUVET (1991) Universal primers for amplificationof three non-coding regions of chloroplast DNA - Plant Mol Biol 17 1105-1109

TSUBOTA H Y AGENO B ESTEacuteBANEZ T YAMAGUCHI amp H DEGUCHI (2003)Molecular phylogeny of the Grimmiales (Musci) based on chloroplast rbcL sequences - Hikobia 1455-70

TSUBOTA H E DE LUNA D GONZAacuteLEZ MS IGNATOV amp H DEGUCHI (2004) Molecularphylogenetics and ordinal relationships based on analyses of a large-scale data set of 600 rbcLsequences of mosses - Hikobia 14 149-170

VITT DH (1984) Classification of the Bryopsida - In SCHUSTER RM (ed) New Manual ofBryology 2 696-759 Hattori Botanical Laboratory Nichinan Japan

VITT DH B GOFFINET amp T HEDDERSON (1998) 8 The ordinal classification of the mossesquestions and answers for the 1990s - In BATES JW NW ASHTON amp JG DUCKETT (eds)Bryology for the twenty-first century British Bryol Soc pp 113-123

Received 3 September 2007 accepted in revised form 30 October 2007

Page 19: botanica parcial 3

19

GROTH-MALONEK M D PRUCHNER F GREWE amp V KNOOP (2005) Ancestors oftrans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosseswith vascular plants - Mol Biol Evol 22 117-125

HATTORI S amp H INOUE (1958) Preliminary report on Takakia lepidozioides - J Hattori BotLab 19 133-137

HE-NYGREacuteN X A JUSLEacuteN I AHONEN D GLENNY amp S PIIPPO (2006) Illuminating theevolutionary history of liverworts (Marchantiophyta) - towards a natural classification - Cladistics22 1-31

HEDDERSON TAJ DJ MURRAY CJ COX amp TL NOWELL (2004) Phylogeneticrelationships of haplolepideous mosses (Dicranidae) inferred from rps4 gene sequences - Syst Bot29 29-41

LA FARGE C BD MISHER JA WHEELER DP WALL K JOHANNES S SCHAFFERamp AJ SHAW (2000) Phylogenetic relationships within the haplolepideous mosses - Bryologist103 257-276

LA FARGE C AJ SHAW amp DH VITT (2002) The circumscription of the Dicranaceae(Bryopsida) based on the chloroplast regions trnL-trnF and rps4 - Syst Bot 27 435-452

MAGOMBO ZLK (2003) The phylogeny of basal peristomate mosses evidence from cpDNAand implications for peristome evolution - Syst Bot 28 24-38

MCNEILL J FR BARRIE HM BURDET V DEMOULIN DL HAWKSWORTHK MARHOLD DH NICOLSON J PRADO PC SILVA JE SKOG JH WIERSEMA ampNJ TURLAND (2006) International Code of Botanical Nomenclature (Vienna Code) - RegnumVegetabile 146 1-568

MUumlLLER K (2004) PRAP - computation of Bremer support for large data sets - Mol PhylogenetEvol 31 780-782

MUumlLLER K (2005) SeqState - primer design and sequence statistics for phylogenetic DNA datasets - Appl Bioinformatics 4 65-69

MUumlLLER K D QUANDT J MUumlLLER amp C NEINHUIS (2005) PhyDE v0992 PhylogeneticData Editor - httpwwwphydede

MURRAY BM (1988) Systematics of the Andreaeopsida (Bryophyta) two orders with links toTakakia - Nova Hedwigia Beih 90 289-336

NEWTON AE amp RS TANGNEY (eds) (2007) Pleurocarpous mosses systematics and evolutionSystematics Association Special Volume Series 71 CRC Press Boca Raton 434 pp

NEWTON AE CJ COX JG DUCKETT JA WHEELER B GOFFINET TAJ HEDDER-SON amp BD MISHLER (2000) Evolution of the major moss lineages Phylogenetic analyses basedon multiple gene sequences and morphology - Bryologist 103 187-211

NEWTON AE N WIKSTROumlM NE BELL LL FORREST amp MS IGNATOV (2007)Dating the diversification of the pleurocarpous mosses - In NEWTON AE amp RS TANGNEY(eds) Pleurocarpous mosses systematics and evolution Systematics Association Special VolumeSeries 71 337-366

NIXON KC (1999) The parsimony ratchet a new method for rapid parsimony analysis - Cladistics15 407-411

OBRIEN TJ (2007) The phylogenetic distribution of pleurocarpous mosses evidence fromcpDNA sequences - In NEWTON AE amp RS TANGNEY (eds) Pleurocarpous mossessystematics and evolution Systematics Association Special Volume Series 71 19-41

OCHYRA R (2002) Nomenclatural changes in subfamilies of the Dicranaceae - CryptogamieBryol 23 345-349

20

OCHYRA R J ŻARNOWIEC amp H BEDNAREK-OCHYRA (2003) Census catalogue ofPolish mosses - Biodiv Poland 3 1-372

PEDERSEN N amp AE NEWTON (2007) Phylogenetic and morphological studies within thePtychomniales with emphasis on the evolution of dwarf males - In NEWTON AE amp RSTANGNEY (eds) Pleurocarpous mosses systematics and evolution Systematics AssociationSpecial Volume Series 71 367-392

QUANDT D amp M STECH (2005) Molecular evolution and secondary structure of the chloroplasttrnL intron in bryophytes - Mol Phylogenet Evol 36 429-443

QUANDT D K MUumlLLER amp S HUTTUNEN (2003) Characterisation of the chloroplast DNApsbT-H region and the influence of dyad symmetrical elements on phylogenetic reconstructions -Plant Biol 5 400-410

QUANDT D K MUumlLLER M STECH W FREY KW HILU amp T BORSCH (2004) Molecularevolution of the chloroplast trnL-F-region in land plants - In GOFFINET B V HOLLOWELL ampR MAGILL (eds) Molecular systematics of bryophytes Monogr Syst Bot Missouri Bot Gard98 13-37

QUANDT D NE BELL amp M STECH (2007) Unravelling the knot the Pulchrinodaceae famnov (Bryales) - In KUumlRSCHNER H T PFEIFFER amp M STECH (eds) A Festschrift to Wolf-gang Frey - a scientists life between deserts and rain forests Nova Hedwigia Beih 131 21-39

QIU Y-L Y CHO JC COX amp JD PALMER (1998) The gain of three mitochondrial intronsidentifies liverworts as the earliest land plants - Nature 394 671-674

QIU Y-L L LI B WANG Z CHEN V KNOOP M GROTH-MALONEK O DOM-BROVSKA J LEE L KENT J REST GF ESTABROOK TA HENDRY DW TAYLORCM TESTA M AMBROS B CRANDALL-STOTLER J DUFF M STECH W FREYD QUANDT amp CC DAVIS (2006) The deepest divergences in land plants inferred fromphylogenomic evidence - Proc Natl Acad Sci USA 103 15511-15516

RENZAGLIA KS S SCHUETTE RJ DUFF R LIGRONE AJ SHAW BD MISHLER ampJG DUCKETT (2007) Bryophyte phylogeny Advancing the molecular and morphological frontiers- Bryologist 110 179-213

SAMIGULLIN TH SP YACENTYUK GV DEGTYARYEVA KM VALIEJO-ROMANVK BOBROVA I CAPESIUS WF MARTIN AV TROITSKY VR FILIN amp ASANTONOV (2002) Paraphyly of bryophytes and close relationships of hornworts and vascularplants inferred from analysis of chloroplast rDNA ITS (cpITS) sequences - Arctoa 11 31-43

SANG T DJ CRAWFORD amp TF STUESSY (1997) Chloroplast DNA phylogeny reticulateevolution and biogeography of Paeonia (Paeoniaceae) - Amer J Bot 84 1120-1136

SHAW AJ amp KS RENZAGLIA (2004) Phylogeny and diversification of bryophytes - AmerJ Bot 91 1557-1581

SHAW AJ CJ COX amp B GOFFINET (2005) Global patterns of moss diversity taxonomic andmolecular inferences - Taxon 54 337-352

STECH M (1999a) A reclassification of Dicranaceae (Bryopsida) based on non-coding cpDNAsequence data - J Hattori Bot Lab 86 137-159

STECH M (1999b) A molecular systematic contribution to the position of Amphidium Schimp(Rhabdoweisiaceae Bryopsida) - Nova Hedwigia 68 291-300

STECH M (2004) Supraspecific circumscription and classification of Campylopus Brid(Dicranaceae Bryopsida) based on molecular data - Syst Bot 29 817-824

STECH M amp D QUANDT (2006) Molecular evolution of the chloroplast atpB-rbcL spacer inbryophytes - In SHARMA AK amp A SHARMA (eds) Plant Genome Biodiversity and EvolutionVol 2 Part B pp 409-431 Science Publishers Enfield New Hampshire

21

STECH M D QUANDT amp W FREY (2003) Molecular circumscription of the hornworts(Antho-cerotophyta) based on the chloroplast DNA trnL-trnF region - J Plant Res 116 389-398

STOTLER RE amp B CRANDALL-STOTLER (2005) A revised classification of theAnthocerotophyta and a checklist of the hornworts of North America north of Mexico - Bryologist108 16-26

SWOFFORD DL (2002) PAUP Phylogenetic analysis using parsimony (and other methods)version 40b10 - Sunderland MA

TABERLET P L GIELLY G PAUTOU amp J BOUVET (1991) Universal primers for amplificationof three non-coding regions of chloroplast DNA - Plant Mol Biol 17 1105-1109

TSUBOTA H Y AGENO B ESTEacuteBANEZ T YAMAGUCHI amp H DEGUCHI (2003)Molecular phylogeny of the Grimmiales (Musci) based on chloroplast rbcL sequences - Hikobia 1455-70

TSUBOTA H E DE LUNA D GONZAacuteLEZ MS IGNATOV amp H DEGUCHI (2004) Molecularphylogenetics and ordinal relationships based on analyses of a large-scale data set of 600 rbcLsequences of mosses - Hikobia 14 149-170

VITT DH (1984) Classification of the Bryopsida - In SCHUSTER RM (ed) New Manual ofBryology 2 696-759 Hattori Botanical Laboratory Nichinan Japan

VITT DH B GOFFINET amp T HEDDERSON (1998) 8 The ordinal classification of the mossesquestions and answers for the 1990s - In BATES JW NW ASHTON amp JG DUCKETT (eds)Bryology for the twenty-first century British Bryol Soc pp 113-123

Received 3 September 2007 accepted in revised form 30 October 2007

Page 20: botanica parcial 3

20

OCHYRA R J ŻARNOWIEC amp H BEDNAREK-OCHYRA (2003) Census catalogue ofPolish mosses - Biodiv Poland 3 1-372

PEDERSEN N amp AE NEWTON (2007) Phylogenetic and morphological studies within thePtychomniales with emphasis on the evolution of dwarf males - In NEWTON AE amp RSTANGNEY (eds) Pleurocarpous mosses systematics and evolution Systematics AssociationSpecial Volume Series 71 367-392

QUANDT D amp M STECH (2005) Molecular evolution and secondary structure of the chloroplasttrnL intron in bryophytes - Mol Phylogenet Evol 36 429-443

QUANDT D K MUumlLLER amp S HUTTUNEN (2003) Characterisation of the chloroplast DNApsbT-H region and the influence of dyad symmetrical elements on phylogenetic reconstructions -Plant Biol 5 400-410

QUANDT D K MUumlLLER M STECH W FREY KW HILU amp T BORSCH (2004) Molecularevolution of the chloroplast trnL-F-region in land plants - In GOFFINET B V HOLLOWELL ampR MAGILL (eds) Molecular systematics of bryophytes Monogr Syst Bot Missouri Bot Gard98 13-37

QUANDT D NE BELL amp M STECH (2007) Unravelling the knot the Pulchrinodaceae famnov (Bryales) - In KUumlRSCHNER H T PFEIFFER amp M STECH (eds) A Festschrift to Wolf-gang Frey - a scientists life between deserts and rain forests Nova Hedwigia Beih 131 21-39

QIU Y-L Y CHO JC COX amp JD PALMER (1998) The gain of three mitochondrial intronsidentifies liverworts as the earliest land plants - Nature 394 671-674

QIU Y-L L LI B WANG Z CHEN V KNOOP M GROTH-MALONEK O DOM-BROVSKA J LEE L KENT J REST GF ESTABROOK TA HENDRY DW TAYLORCM TESTA M AMBROS B CRANDALL-STOTLER J DUFF M STECH W FREYD QUANDT amp CC DAVIS (2006) The deepest divergences in land plants inferred fromphylogenomic evidence - Proc Natl Acad Sci USA 103 15511-15516

RENZAGLIA KS S SCHUETTE RJ DUFF R LIGRONE AJ SHAW BD MISHLER ampJG DUCKETT (2007) Bryophyte phylogeny Advancing the molecular and morphological frontiers- Bryologist 110 179-213

SAMIGULLIN TH SP YACENTYUK GV DEGTYARYEVA KM VALIEJO-ROMANVK BOBROVA I CAPESIUS WF MARTIN AV TROITSKY VR FILIN amp ASANTONOV (2002) Paraphyly of bryophytes and close relationships of hornworts and vascularplants inferred from analysis of chloroplast rDNA ITS (cpITS) sequences - Arctoa 11 31-43

SANG T DJ CRAWFORD amp TF STUESSY (1997) Chloroplast DNA phylogeny reticulateevolution and biogeography of Paeonia (Paeoniaceae) - Amer J Bot 84 1120-1136

SHAW AJ amp KS RENZAGLIA (2004) Phylogeny and diversification of bryophytes - AmerJ Bot 91 1557-1581

SHAW AJ CJ COX amp B GOFFINET (2005) Global patterns of moss diversity taxonomic andmolecular inferences - Taxon 54 337-352

STECH M (1999a) A reclassification of Dicranaceae (Bryopsida) based on non-coding cpDNAsequence data - J Hattori Bot Lab 86 137-159

STECH M (1999b) A molecular systematic contribution to the position of Amphidium Schimp(Rhabdoweisiaceae Bryopsida) - Nova Hedwigia 68 291-300

STECH M (2004) Supraspecific circumscription and classification of Campylopus Brid(Dicranaceae Bryopsida) based on molecular data - Syst Bot 29 817-824

STECH M amp D QUANDT (2006) Molecular evolution of the chloroplast atpB-rbcL spacer inbryophytes - In SHARMA AK amp A SHARMA (eds) Plant Genome Biodiversity and EvolutionVol 2 Part B pp 409-431 Science Publishers Enfield New Hampshire

21

STECH M D QUANDT amp W FREY (2003) Molecular circumscription of the hornworts(Antho-cerotophyta) based on the chloroplast DNA trnL-trnF region - J Plant Res 116 389-398

STOTLER RE amp B CRANDALL-STOTLER (2005) A revised classification of theAnthocerotophyta and a checklist of the hornworts of North America north of Mexico - Bryologist108 16-26

SWOFFORD DL (2002) PAUP Phylogenetic analysis using parsimony (and other methods)version 40b10 - Sunderland MA

TABERLET P L GIELLY G PAUTOU amp J BOUVET (1991) Universal primers for amplificationof three non-coding regions of chloroplast DNA - Plant Mol Biol 17 1105-1109

TSUBOTA H Y AGENO B ESTEacuteBANEZ T YAMAGUCHI amp H DEGUCHI (2003)Molecular phylogeny of the Grimmiales (Musci) based on chloroplast rbcL sequences - Hikobia 1455-70

TSUBOTA H E DE LUNA D GONZAacuteLEZ MS IGNATOV amp H DEGUCHI (2004) Molecularphylogenetics and ordinal relationships based on analyses of a large-scale data set of 600 rbcLsequences of mosses - Hikobia 14 149-170

VITT DH (1984) Classification of the Bryopsida - In SCHUSTER RM (ed) New Manual ofBryology 2 696-759 Hattori Botanical Laboratory Nichinan Japan

VITT DH B GOFFINET amp T HEDDERSON (1998) 8 The ordinal classification of the mossesquestions and answers for the 1990s - In BATES JW NW ASHTON amp JG DUCKETT (eds)Bryology for the twenty-first century British Bryol Soc pp 113-123

Received 3 September 2007 accepted in revised form 30 October 2007

Page 21: botanica parcial 3

21

STECH M D QUANDT amp W FREY (2003) Molecular circumscription of the hornworts(Antho-cerotophyta) based on the chloroplast DNA trnL-trnF region - J Plant Res 116 389-398

STOTLER RE amp B CRANDALL-STOTLER (2005) A revised classification of theAnthocerotophyta and a checklist of the hornworts of North America north of Mexico - Bryologist108 16-26

SWOFFORD DL (2002) PAUP Phylogenetic analysis using parsimony (and other methods)version 40b10 - Sunderland MA

TABERLET P L GIELLY G PAUTOU amp J BOUVET (1991) Universal primers for amplificationof three non-coding regions of chloroplast DNA - Plant Mol Biol 17 1105-1109

TSUBOTA H Y AGENO B ESTEacuteBANEZ T YAMAGUCHI amp H DEGUCHI (2003)Molecular phylogeny of the Grimmiales (Musci) based on chloroplast rbcL sequences - Hikobia 1455-70

TSUBOTA H E DE LUNA D GONZAacuteLEZ MS IGNATOV amp H DEGUCHI (2004) Molecularphylogenetics and ordinal relationships based on analyses of a large-scale data set of 600 rbcLsequences of mosses - Hikobia 14 149-170

VITT DH (1984) Classification of the Bryopsida - In SCHUSTER RM (ed) New Manual ofBryology 2 696-759 Hattori Botanical Laboratory Nichinan Japan

VITT DH B GOFFINET amp T HEDDERSON (1998) 8 The ordinal classification of the mossesquestions and answers for the 1990s - In BATES JW NW ASHTON amp JG DUCKETT (eds)Bryology for the twenty-first century British Bryol Soc pp 113-123

Received 3 September 2007 accepted in revised form 30 October 2007